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RNA polymerase II large subunit [Arabidopsis thaliana]
Protein Classification
DNA-directed RNA polymerase II subunit RPB1 ( domain architecture ID 10119612 )
DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
18-872
0e+00
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain]
Cd Length: 751
Bit Score: 1532.86
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 18 VQFGILSPDEIR Q MSV IHV EH S ET T E K G K - PK V GGL S D T R L GTIDR KVK C E TC MAN M A ECPGHFG YL ELAKP MY H V GF MK 96
Cdd:cd02733 3 VQFGILSPDEIR A MSV AEI EH P ET Y E N G G g PK L GGL N D P R M GTIDR NSR C Q TC GGD M K ECPGHFG HI ELAKP VF H I GF LT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 97 TV L S I M RCVC fncskiladeeehkfkqamkiknpknrlkkildacknktkcdggddiddvqshstdepvkksrggcgaqq 176
Cdd:cd02733 83 KI L K I L RCVC ---------------------------------------------------------------------- 92
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 177 pkltiegmkmiaeykiqrkkndepdqlpepaer K QT L G A D RVL SVL KRISD A DC QL LGF N PKF A RPDWMIL E VLP I PPP P 256
Cdd:cd02733 93 --------------------------------- K RE L S A E RVL EIF KRISD E DC RI LGF D PKF S RPDWMIL T VLP V PPP A 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 257 VRPSV M MD ATS RSEDDLTH Q LA M II RH N EN LKRQE K NGAPAHII S E FT QLLQFH I ATY F DNE L PG Q P R ATQKSGRP I KSI 336
Cdd:cd02733 140 VRPSV V MD GSA RSEDDLTH K LA D II KA N NQ LKRQE Q NGAPAHII E E DE QLLQFH V ATY M DNE I PG L P Q ATQKSGRP L KSI 219
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 337 CS RLK A KEGRIRGNLMGKRVDFSARTVITPDP TINI D EL GVP W SIA L NLT Y PE T VTP Y NI E RL K ELV DY GP HPP PG ktg A 416
Cdd:cd02733 220 RQ RLK G KEGRIRGNLMGKRVDFSARTVITPDP NLEL D QV GVP R SIA M NLT F PE I VTP F NI D RL Q ELV RN GP NEY PG --- A 296
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 417 KYIIRDDG Q R L DLRYLKK S SD Q HL EL GY K VERHLQDGD F VLFNRQPSLHKMS I MGHR IRIM PYSTFRLNLSVT S PYNADF 496
Cdd:cd02733 297 KYIIRDDG E R I DLRYLKK A SD L HL QY GY I VERHLQDGD V VLFNRQPSLHKMS M MGHR VKVL PYSTFRLNLSVT T PYNADF 376
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 497 DGDEMN M HVPQS F ETRAE VL ELMMVP KC IVSPQ A N R PVMGIVQDTLLG C RK I TKRDTF I EKD VF MN T LMW WE D F DGK V P A 576
Cdd:cd02733 377 DGDEMN L HVPQS L ETRAE LK ELMMVP RQ IVSPQ S N K PVMGIVQDTLLG V RK L TKRDTF L EKD QV MN L LMW LP D W DGK I P Q 456
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 577 PAILKP R PLWTGKQ V F N LIIPK QI NL L R Y S AW H a D TETGF I T PGDT Q V R IE R GELL A G T LCKKT L G T S N G S L V HVIW E E V 656
Cdd:cd02733 457 PAILKP K PLWTGKQ I F S LIIPK IN NL I R S S SH H - D GDKKW I S PGDT K V I IE N GELL S G I LCKKT V G A S S G G L I HVIW L E Y 535
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 657 GP D AAR K F L G HT Q WL VN Y WLL Q NGF T IGIGDTIAD SS TM E KI N ETI SN AK TA V KD LI RQF Q GK EL D P E PG R T M R DT FEN R 736
Cdd:cd02733 536 GP E AAR D F I G NI Q RV VN N WLL H NGF S IGIGDTIAD KE TM K KI Q ETI KK AK RD V IK LI EKA Q NG EL E P Q PG K T L R ES FEN K 615
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 737 VN QV LNKARD D AG S SAQKSL A E T NN L KAMVTAGSKGSFINISQ MT ACVGQQNVEGKRIPFGF DG RTLPHF T KDDYGPESR 816
Cdd:cd02733 616 VN RI LNKARD K AG K SAQKSL S E D NN F KAMVTAGSKGSFINISQ II ACVGQQNVEGKRIPFGF RR RTLPHF I KDDYGPESR 695
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 334187204 817 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT S ETGYIQRRLVKAMED I MVKYD 872
Cdd:cd02733 696 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT A ETGYIQRRLVKAMED V MVKYD 751
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1055-1467
0e+00
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain]
Cd Length: 410
Bit Score: 798.34
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1055 Y K L SR EAF E W VI GEIE S RF LQ SLV A PGEM I G CV AAQSIGEPATQMTLNTFH Y AGVSAKNVTLGVPRL R EIINVAK R IKTP 1134
Cdd:cd02584 1 Y R L NK EAF D W IL GEIE T RF NR SLV H PGEM V G TI AAQSIGEPATQMTLNTFH F AGVSAKNVTLGVPRL K EIINVAK N IKTP 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1135 SL S VYL T P EAS K SK E G AK TV Q CA LE Y TTL RS VT Q ATE VW YDPDP MS T I IEED F EFV R SY Y E M PDEDV SP D KI SPWLLRIE 1214
Cdd:cd02584 81 SL T VYL E P GFA K DE E K AK KI Q SR LE H TTL KD VT A ATE IY YDPDP QN T V IEED K EFV E SY F E F PDEDV EQ D RL SPWLLRIE 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1215 L N R EM M V DKKLSM AD IA E KI NL EF D DDL TC IF N DDNA Q KL IL RIRI M ND EGP K G E LQ desa EDDVFLKKIESNML TE M A L 1294
Cdd:cd02584 161 L D R KK M T DKKLSM EQ IA K KI KE EF K DDL NV IF S DDNA E KL VI RIRI I ND DEE K E E DS ---- EDDVFLKKIESNML SD M T L 236
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1295 R GI PD I N KVFI KQVR K SRF D - E E G G FK TS EEW M L D T E GVNL LA V MC H ED VDP K RTTSN HLI EI I EVLGIEA V R R ALL D EL 1373
Cdd:cd02584 237 K GI EG I R KVFI REEN K KKV D i E T G E FK KR EEW V L E T D GVNL RE V LS H PG VDP T RTTSN DIV EI F EVLGIEA A R K ALL K EL 316
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1374 R V VISFDGSYVNYRHLA I LCD T MT Y RGHLMAITRHGINR N DTGPLMRCSFEETVDILL D AAA YA ETD C L R GV T ENIMLGQ 1453
Cdd:cd02584 317 R N VISFDGSYVNYRHLA L LCD V MT Q RGHLMAITRHGINR Q DTGPLMRCSFEETVDILL E AAA FG ETD D L K GV S ENIMLGQ 396
410
....*....|....
gi 334187204 1454 LAPIGTG DCE L Y L N 1467
Cdd:cd02584 397 LAPIGTG CFD L L L D 410
RNA_pol_Rpb1_6
pfam04992 RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
892-1076
1.51e-93
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511
Cd Length: 188
Bit Score: 300.57
E-value: 1.51e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 892 M D AVW IE S QK L D S LK MKKSE F DRTFKYEID DE NWN -- P T YL SDEHLEDLK G IR E LRDVF D A EY SK L ET DR FQ L GTE I ATN 969
Cdd:pfam04992 1 L D GAF IE K QK I D T LK LSDAA F EKRYRLDVM DE KSG fl P G YL EEGVIKEIA G DP E VQQLL D E EY EQ L LE DR EL L REI I FPT 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 970 GDS TW P - LPVNI K R H I W NAQK T F K ID L RK I SD M HP VEIVDA V DK L QE RL L VV P GDD A LS V EAQ K NATL F F N ILLRS T LAS 1048
Cdd:pfam04992 81 GDS KV P q LPVNI Q R I I Q NAQK I F H ID D RK P SD L HP IYVIEG V RE L LD RL V VV R GDD P LS K EAQ E NATL L F K ILLRS R LAS 160
170 180
....*....|....*....|....*...
gi 334187204 1049 KRVLEEY K L SR EAF E WV I GEIESRFLQ S 1076
Cdd:pfam04992 161 KRVLEEY R L NK EAF D WV L GEIESRFLQ A 188
Name
Accession
Description
Interval
E-value
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
18-872
0e+00
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain]
Cd Length: 751
Bit Score: 1532.86
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 18 VQFGILSPDEIR Q MSV IHV EH S ET T E K G K - PK V GGL S D T R L GTIDR KVK C E TC MAN M A ECPGHFG YL ELAKP MY H V GF MK 96
Cdd:cd02733 3 VQFGILSPDEIR A MSV AEI EH P ET Y E N G G g PK L GGL N D P R M GTIDR NSR C Q TC GGD M K ECPGHFG HI ELAKP VF H I GF LT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 97 TV L S I M RCVC fncskiladeeehkfkqamkiknpknrlkkildacknktkcdggddiddvqshstdepvkksrggcgaqq 176
Cdd:cd02733 83 KI L K I L RCVC ---------------------------------------------------------------------- 92
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 177 pkltiegmkmiaeykiqrkkndepdqlpepaer K QT L G A D RVL SVL KRISD A DC QL LGF N PKF A RPDWMIL E VLP I PPP P 256
Cdd:cd02733 93 --------------------------------- K RE L S A E RVL EIF KRISD E DC RI LGF D PKF S RPDWMIL T VLP V PPP A 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 257 VRPSV M MD ATS RSEDDLTH Q LA M II RH N EN LKRQE K NGAPAHII S E FT QLLQFH I ATY F DNE L PG Q P R ATQKSGRP I KSI 336
Cdd:cd02733 140 VRPSV V MD GSA RSEDDLTH K LA D II KA N NQ LKRQE Q NGAPAHII E E DE QLLQFH V ATY M DNE I PG L P Q ATQKSGRP L KSI 219
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 337 CS RLK A KEGRIRGNLMGKRVDFSARTVITPDP TINI D EL GVP W SIA L NLT Y PE T VTP Y NI E RL K ELV DY GP HPP PG ktg A 416
Cdd:cd02733 220 RQ RLK G KEGRIRGNLMGKRVDFSARTVITPDP NLEL D QV GVP R SIA M NLT F PE I VTP F NI D RL Q ELV RN GP NEY PG --- A 296
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 417 KYIIRDDG Q R L DLRYLKK S SD Q HL EL GY K VERHLQDGD F VLFNRQPSLHKMS I MGHR IRIM PYSTFRLNLSVT S PYNADF 496
Cdd:cd02733 297 KYIIRDDG E R I DLRYLKK A SD L HL QY GY I VERHLQDGD V VLFNRQPSLHKMS M MGHR VKVL PYSTFRLNLSVT T PYNADF 376
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 497 DGDEMN M HVPQS F ETRAE VL ELMMVP KC IVSPQ A N R PVMGIVQDTLLG C RK I TKRDTF I EKD VF MN T LMW WE D F DGK V P A 576
Cdd:cd02733 377 DGDEMN L HVPQS L ETRAE LK ELMMVP RQ IVSPQ S N K PVMGIVQDTLLG V RK L TKRDTF L EKD QV MN L LMW LP D W DGK I P Q 456
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 577 PAILKP R PLWTGKQ V F N LIIPK QI NL L R Y S AW H a D TETGF I T PGDT Q V R IE R GELL A G T LCKKT L G T S N G S L V HVIW E E V 656
Cdd:cd02733 457 PAILKP K PLWTGKQ I F S LIIPK IN NL I R S S SH H - D GDKKW I S PGDT K V I IE N GELL S G I LCKKT V G A S S G G L I HVIW L E Y 535
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 657 GP D AAR K F L G HT Q WL VN Y WLL Q NGF T IGIGDTIAD SS TM E KI N ETI SN AK TA V KD LI RQF Q GK EL D P E PG R T M R DT FEN R 736
Cdd:cd02733 536 GP E AAR D F I G NI Q RV VN N WLL H NGF S IGIGDTIAD KE TM K KI Q ETI KK AK RD V IK LI EKA Q NG EL E P Q PG K T L R ES FEN K 615
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 737 VN QV LNKARD D AG S SAQKSL A E T NN L KAMVTAGSKGSFINISQ MT ACVGQQNVEGKRIPFGF DG RTLPHF T KDDYGPESR 816
Cdd:cd02733 616 VN RI LNKARD K AG K SAQKSL S E D NN F KAMVTAGSKGSFINISQ II ACVGQQNVEGKRIPFGF RR RTLPHF I KDDYGPESR 695
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 334187204 817 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT S ETGYIQRRLVKAMED I MVKYD 872
Cdd:cd02733 696 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT A ETGYIQRRLVKAMED V MVKYD 751
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
8-893
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 989.36
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 8 S P AEVSKVR vvq FG I LSP D EIR Q MSV IHVEHSE T - TEK G K P KV GGL S D T RLG T ID RKVK C E TC MANMA ECPGHFG YL ELA 86
Cdd:PRK08566 5 I P KRIGSIK --- FG L LSP E EIR K MSV TKIITAD T y DDD G Y P ID GGL M D P RLG V ID PGLR C K TC GGRAG ECPGHFG HI ELA 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 87 K P MY HVGF M K TVLSIM R CV C FN C SKILAD EEE hkfkqamkiknp KNRLKKI L DAC K NK tkcdg G DDI DD VQSHSTD E PV K 166
Cdd:PRK08566 82 R P VI HVGF A K LIYKLL R AT C RE C GRLKLT EEE ------------ IEEYLEK L ERL K EW ----- G SLA DD LIKEVKK E AA K 144
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 167 KSR - GG CG AQ Q P K LTI E gm K MI a EYKIQ RK KNDE pd Q L p E P AE rkqtlgadr VLSV L KR I S D A D CQ LLG F NP KF ARP D WM 245
Cdd:PRK08566 145 RMV c PH CG EK Q Y K IKF E -- K PT - TFYEE RK EGLV -- K L - T P SD --------- IRER L EK I P D E D LE LLG I NP EV ARP E WM 209
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 246 I L E VLP I PP PP VRPS VMMDATS RSEDDLTH Q L AM IIR H N EN LK RQEKN GAP AH II SEFTQ LLQ F H IA TYFDNE L PG Q P R A 325
Cdd:PRK08566 210 V L T VLP V PP VT VRPS ITLETGQ RSEDDLTH K L VD IIR I N QR LK ENIEA GAP QL II EDLWE LLQ Y H VT TYFDNE I PG I P P A 289
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 326 TQK SGRP I K SICS RLK A KEGR I RGNL M GKRV D FSARTVI T PDP TIN I D E L GVP WS IA LN LT Y PE T VT PY NIE R L K E L V DY 405
Cdd:PRK08566 290 RHR SGRP L K TLAQ RLK G KEGR F RGNL S GKRV N FSARTVI S PDP NLS I N E V GVP EA IA KE LT V PE R VT EW NIE E L R E Y V LN 369
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 406 GP HPP PG ktg A K Y I IR D DG Q R LD L RYL - K KSSDQH LE L G YK VERHL Q DGD F VLFNRQPSLH K MSIM G HR I R IM P YS TFRL 484
Cdd:PRK08566 370 GP EKH PG --- A N Y V IR P DG R R IK L TDK n K EELAEK LE P G WI VERHL I DGD I VLFNRQPSLH R MSIM A HR V R VL P GK TFRL 446
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 485 NL S V TS PYNADFDGDEMN M HVPQ SF E T RAE VLE LM M V PKC I V SP QANR P VM G IV QD TLL G CRKI T KRD T FIE K DVFMNT L 564
Cdd:PRK08566 447 NL A V CP PYNADFDGDEMN L HVPQ TE E A RAE ARI LM L V QEH I L SP RYGG P II G GI QD HIS G AYLL T RKS T LFT K EEALDL L 526
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 565 MWWEDFDGKV P A PAI LKPR P L WTGKQ V F N L II PK QI NL l RYS A --- WHA D TETGFITPG D TQ V R I ER G E LL A G TLC KK TL 641
Cdd:PRK08566 527 RAAGIDELPE P E PAI ENGK P Y WTGKQ I F S L FL PK DL NL - EFK A kic SGC D ECKKEDCEH D AY V V I KN G K LL E G VID KK AI 605
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 642 G TSN GS LVHV I WE E V GP DA AR K FL GHTQW L VNYWLLQN GFT I GI G D TIADSSTM E K I N E T I SN A KTA V KD LI RQFQGK EL 721
Cdd:PRK08566 606 G AEQ GS ILDR I VK E Y GP ER AR R FL DSVTR L AIRFIMLR GFT T GI D D EDIPEEAK E E I D E I I EE A EKR V EE LI EAYENG EL 685
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 722 D P E PGRT MRD T F E NRVN QVL N KARD D AG SS A Q K S L AET N NLKA M VTA G SK GS FI N IS QM T ACVGQQ N V E G K RI PF G FDG R 801
Cdd:PRK08566 686 E P L PGRT LEE T L E MKIM QVL G KARD E AG EI A E K Y L GLD N PAVI M ART G AR GS ML N LT QM A ACVGQQ S V R G E RI RR G YRD R 765
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 802 TLPHF TKD D Y G P E S RGFV EN SY LR GLTP Q EFFFHAMGGREGL I DTAV K TS ET GY I QRRL VK A ME D IM V K YDGTVR NSL G D 881
Cdd:PRK08566 766 TLPHF KPG D L G A E A RGFV RS SY KS GLTP T EFFFHAMGGREGL V DTAV R TS QS GY M QRRL IN A LQ D LK V E YDGTVR DTR G N 845
890
....*....|..
gi 334187204 882 VI QF L YGEDG M D 893
Cdd:PRK08566 846 IV QF K YGEDG V D 857
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
14-893
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 937.99
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 14 K VRVVQ FG I LSP D EIR Q MSV IH V EHSE T - TEK G K P KV GGL S D T RLG T I DRKVK C E TC MANMA ECPGHFG YL ELA K P MY HV 92
Cdd:TIGR02390 3 K IGSIK FG L LSP E EIR K MSV VE V VTAD T y DDD G Y P IE GGL M D P RLG V I EPGLR C K TC GGKVG ECPGHFG HI ELA R P VV HV 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 93 GF M K TVLS I M R CV C FN C SK I LAD EEE hkfkqamkiknp KNRLKKILDAC K NKTKCDGGDD I DDVQSHSTDEPVKKS rgg C 172
Cdd:TIGR02390 83 GF A K EIYK I L R AT C RK C GR I TLT EEE ------------ IEQYLEKINKL K EEGGDLASTL I EKIVKEAAKRMKCPH --- C 147
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 173 G AQ Q P K LTI E gmk MIAEYKIQR K KN D EPDQLP E PA ER kqtlgadrvlsv L KR I S D A D CQ LLG F NPK F ARP D WM I L E VLP I 252
Cdd:TIGR02390 148 G EE Q K K IKF E --- KPTYFYEEG K EG D VKLTPS E IR ER ------------ L EK I P D E D AE LLG I NPK V ARP E WM V L T VLP V 212
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 253 PP PP VRPS VMMDATS RSEDDLTH Q L AM IIR H N EN LK RQEKN GAP AH II SEFTQ LLQ F H I ATYFDNELPG Q P R A TQK SGRP 332
Cdd:TIGR02390 213 PP VT VRPS ITLETGE RSEDDLTH K L VD IIR I N QR LK ENIEA GAP QL II EDLWE LLQ Y H V ATYFDNELPG I P P A RHR SGRP 292
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 333 I K SICS RLK A KEGR I RGNL M GKRV D FSARTVI T PDP T I N I D E L GVP WS IA LN LT Y PE T VTP Y NI ER L K E L V DY GP HPP PG 412
Cdd:TIGR02390 293 L K TLAQ RLK G KEGR F RGNL S GKRV N FSARTVI S PDP N I S I N E V GVP EQ IA KE LT V PE R VTP W NI DE L R E Y V LN GP DSW PG 372
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 413 ktg A K Y I IR D DG Q R LDL R YLK K SS - DQH LE L G YK VERHL Q DGD F VLFNRQPSLH K MS I MGH RIRIM P YS TFRLNL S V TS P 491
Cdd:TIGR02390 373 --- A N Y V IR P DG R R IKI R DEN K EE l AER LE P G WV VERHL I DGD I VLFNRQPSLH R MS M MGH KVKVL P GK TFRLNL A V CP P 449
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 492 YNADFDGDEMN M HVPQ SF E T RAE VL ELM M V PKC I VS P QANR P VM G IVQ D TLL G CRKI T KRD T FIE K DV f MN T LMWWEDFD 571
Cdd:TIGR02390 450 YNADFDGDEMN L HVPQ TE E A RAE AR ELM L V EEH I LT P RYGG P II G GIH D YIS G AYLL T HKS T LFT K EE - VQ T ILGVAGYF 528
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 572 G KV P A PAI L KP RPL WTGKQ V F NLII P KQI N LLRYSAWHADTET -- GFIT P G D TQ V R I ER G E LL A G TLC KK TL G TSN G SLV 649
Cdd:TIGR02390 529 G DP P E PAI E KP KEY WTGKQ I F SAFL P EDL N FEGRAKICSGSDA ck KEEC P H D AY V V I KN G K LL K G VID KK AI G AEK G KIL 608
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 650 H V I WE E V GP D AAR K FL GHTQW L VNYWLLQN GFT I GI G D TIADSSTM E K I N E T I SN A KTA V KD LI RQFQGK EL D P E PGRT M 729
Cdd:TIGR02390 609 H R I VR E Y GP E AAR R FL DSVTR L FIRFITLR GFT T GI D D IDIPKEAK E E I E E L I EK A EKR V DN LI ERYRNG EL E P L PGRT V 688
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 730 RD T F E NRVNQ VL N KARD D AG SS A Q K S L AET N NLKA M VTA G SK GS FI NI S QM T A C VGQQ N V E G K RI PF G FDG RTLPHF T K D 809
Cdd:TIGR02390 689 EE T L E MKIME VL G KARD E AG EV A E K Y L DPE N HAVI M ART G AR GS LL NI T QM A A M VGQQ S V R G G RI RR G YRN RTLPHF K K G 768
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 810 D Y G PES RGFV EN S YLR GL T P Q E F FFHA M GGREGL I DTAV K TS ET GY I QRRL VK A ME D IM V K YDGTVR NSL G DV IQF L YGE 889
Cdd:TIGR02390 769 D I G AKA RGFV RS S FKK GL D P T E Y FFHA A GGREGL V DTAV R TS QS GY M QRRL IN A LQ D LY V E YDGTVR DTR G NL IQF K YGE 848
....
gi 334187204 890 DG M D 893
Cdd:TIGR02390 849 DG V D 852
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1055-1467
0e+00
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain]
Cd Length: 410
Bit Score: 798.34
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1055 Y K L SR EAF E W VI GEIE S RF LQ SLV A PGEM I G CV AAQSIGEPATQMTLNTFH Y AGVSAKNVTLGVPRL R EIINVAK R IKTP 1134
Cdd:cd02584 1 Y R L NK EAF D W IL GEIE T RF NR SLV H PGEM V G TI AAQSIGEPATQMTLNTFH F AGVSAKNVTLGVPRL K EIINVAK N IKTP 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1135 SL S VYL T P EAS K SK E G AK TV Q CA LE Y TTL RS VT Q ATE VW YDPDP MS T I IEED F EFV R SY Y E M PDEDV SP D KI SPWLLRIE 1214
Cdd:cd02584 81 SL T VYL E P GFA K DE E K AK KI Q SR LE H TTL KD VT A ATE IY YDPDP QN T V IEED K EFV E SY F E F PDEDV EQ D RL SPWLLRIE 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1215 L N R EM M V DKKLSM AD IA E KI NL EF D DDL TC IF N DDNA Q KL IL RIRI M ND EGP K G E LQ desa EDDVFLKKIESNML TE M A L 1294
Cdd:cd02584 161 L D R KK M T DKKLSM EQ IA K KI KE EF K DDL NV IF S DDNA E KL VI RIRI I ND DEE K E E DS ---- EDDVFLKKIESNML SD M T L 236
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1295 R GI PD I N KVFI KQVR K SRF D - E E G G FK TS EEW M L D T E GVNL LA V MC H ED VDP K RTTSN HLI EI I EVLGIEA V R R ALL D EL 1373
Cdd:cd02584 237 K GI EG I R KVFI REEN K KKV D i E T G E FK KR EEW V L E T D GVNL RE V LS H PG VDP T RTTSN DIV EI F EVLGIEA A R K ALL K EL 316
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1374 R V VISFDGSYVNYRHLA I LCD T MT Y RGHLMAITRHGINR N DTGPLMRCSFEETVDILL D AAA YA ETD C L R GV T ENIMLGQ 1453
Cdd:cd02584 317 R N VISFDGSYVNYRHLA L LCD V MT Q RGHLMAITRHGINR Q DTGPLMRCSFEETVDILL E AAA FG ETD D L K GV S ENIMLGQ 396
410
....*....|....
gi 334187204 1454 LAPIGTG DCE L Y L N 1467
Cdd:cd02584 397 LAPIGTG CFD L L L D 410
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
826-1418
0e+00
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 583.93
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 826 GLTPQEFFFH A MGGREGLIDTAVKT S E T GY I QRRLVKA M ED IM V K YD G TVRNS L G DVI QFLYGEDG M D AVW IE S Q KLDSL 905
Cdd:pfam04998 1 GLTPQEFFFH T MGGREGLIDTAVKT A E S GY L QRRLVKA L ED LV V T YD D TVRNS G G EIV QFLYGEDG L D PLK IE K Q GRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 906 KMKKSEFDRT FK Y eiddenwnpt Y L S D EH L ED lkgirelrdvfd A E Y S KL etdrfqlgteiatngdstwplpvnikrhiw 985
Cdd:pfam04998 81 EFSDLKLEDK FK N ---------- D L L D DL L LL ------------ S E F S LS ------------------------------ 108
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 986 naq KTFK I DL R KI sdmhpveivdavdklqerllv VP G D D A LS V EAQ KN ATL F F NI LL R S T L A SKRV LE E YKLSRE AF EWV 1065
Cdd:pfam04998 109 --- YKKE I LV R DS --------------------- KL G R D R LS K EAQ ER ATL L F EL LL K S G L E SKRV RS E LTCNSK AF VCL 164
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1066 IGEIESRFL QSL VA PGE MI G CV AAQSIGEP A TQMTLNTFH Y AGV SA KNVTLGVPRL R EIINV A K R IK T PSL S VYL TP E AS 1145
Cdd:pfam04998 165 LCYGRLLYQ QSL IN PGE AV G II AAQSIGEP G TQMTLNTFH F AGV AS KNVTLGVPRL K EIINV S K N IK S PSL T VYL FD E VG 244
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1146 KSK E G AK T V QC A L E YT TL R SV TQAT E VW YDPDP MS T I I EE D FEF V RSYYEMP DE DV ------ SPDKISPWLL R IELNREM 1219
Cdd:pfam04998 245 REL E K AK K V YG A I E KV TL G SV VESG E IL YDPDP FN T P I IS D VKG V VKFFDII DE VT neeeid PETGLLILVI R LLKILNK 324
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1220 MVD K KLSMAD I AEK I NLEF D DDLTCIFNDDN A QKLILRIR I MN D E G PKGELQDESA E D D VF L KKIESNM L TEMA LRGIP D 1299
Cdd:pfam04998 325 SIK K VVKSEV I PRS I RNKV D EGRDIAIGEIT A FIIKISKK I RQ D T G GLRRVDELFM E E D PK L AILVASL L GNIT LRGIP G 404
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1300 I NKVFIKQVR K srfdeegg F K TSEE W M L D TEGVNLL A V MCHED - VD PK R TT SN HLI EI I E V LGIEA V R R ALL D E L R V V IS 1378
Cdd:pfam04998 405 I KRILVNEDD K -------- G K VEPD W V L E TEGVNLL R V LLVPG f VD AG R IL SN DIH EI L E I LGIEA A R N ALL N E I R N V YR 476
570 580 590 600
....*....|....*....|....*....|....*....|
gi 334187204 1379 F D G S Y V N Y RHL AILC D T MT YR G HL MAI T RHGIN RNDTGP L 1418
Cdd:pfam04998 477 F Q G I Y I N D RHL ELIA D Q MT RK G YI MAI G RHGIN KAELSA L 516
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
243-546
1.02e-160
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 492.42
E-value: 1.02e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 243 D WMIL E VLP I PPP PV RPSV MM D ATSRS EDDLTH Q L AM II RH N EN LKR QEKN GAP AH II SEFTQ LLQ FHIA T YF DNE lp G Q 322
Cdd:smart00663 1 E WMIL T VLP V PPP CL RPSV QL D GGRFA EDDLTH L L RD II KR N NR LKR LLEL GAP SI II RNEKR LLQ EAVD T LI DNE -- G L 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 323 PRA T QKSGRP I KS ICS RLK A KEGR I R G NL M GKRVDFSAR T VITPDP TINID E L GVP WS IAL N LT Y PE T VTP Y NI ER L KE L 402
Cdd:smart00663 79 PRA N QKSGRP L KS LSQ RLK G KEGR F R Q NL L GKRVDFSAR S VITPDP NLKLN E V GVP KE IAL E LT F PE I VTP L NI DK L RK L 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 403 V DY GP hpppgk T GAKYIIR dd G QRLD L RYL KKS - SDQ HL EL G YK VERH LQ DGD F VLFNRQP S LH K MSI MG HR I R IMPYS T 481
Cdd:smart00663 159 V RN GP ------ N GAKYIIR -- G KKTN L KLA KKS k IAN HL KI G DI VERH VI DGD V VLFNRQP T LH R MSI QA HR V R VLEGK T 230
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334187204 482 F RLN LS V T SPYNADFDGDEMN M HVPQS F E T RAE VL ELM M VP KC I V SP QANR P VM G IV QD T LLG CR 546
Cdd:smart00663 231 I RLN PL V C SPYNADFDGDEMN L HVPQS L E A RAE AR ELM L VP NN I L SP KNGK P II G PI QD M LLG LY 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
14-351
3.81e-126
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595
Cd Length: 320
Bit Score: 398.59
E-value: 3.81e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 14 K VRVV QFGI L SP D EIR QM SV IH V EHS ET TEK G -- KP KV GGL S D T R L GTID RKVK CETC MANMAE CPGHFG YL ELAKP MY H 91
Cdd:pfam04997 3 K IKEI QFGI A SP E EIR KW SV GE V TKP ET YNY G sl KP EE GGL L D E R M GTID KDYE CETC GKKKKD CPGHFG HI ELAKP VF H 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 92 V GF M K TV L S I MR CVC FN CSK I L A D EEEH ---- K F K QAMKIK N P K NRL K K IL DA CK N K TK C DGGDDID dvqshstdepvkk 167
Cdd:pfam04997 83 I GF F K KT L K I LE CVC KY CSK L L L D PGKP klfn K D K KRLGLE N L K MGA K A IL EL CK K K DL C EHCGGKN ------------- 149
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 168 sr G G CG A QQP KLTI EG M K MI A ey K I QRK K ND E P dqlpepaer K QT L GADR VL SVL KRISD A D CQL LGFNP KFA RP D WMIL 247
Cdd:pfam04997 150 -- G V CG S QQP VSRK EG L K LK A -- A I KKS K EE E E --------- K EI L NPEK VL KIF KRISD E D VEI LGFNP SGS RP E WMIL 216
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 248 E VLP I PPP PV RPSV MM D ATS R S EDDLTH Q L AM II RH N EN LK RQEKN GAP A HII S E FTQ LLQ F H I AT Y FDNE L PG Q P R A T Q 327
Cdd:pfam04997 217 T VLP V PPP CI RPSV QL D GGR R A EDDLTH K L RD II KR N NR LK KLLEL GAP S HII R E EWR LLQ E H V AT L FDNE I PG L P P A L Q 296
330 340
....*....|....*....|....
gi 334187204 328 KS G RP I KSI CS RLK A KEGR I RGNL 351
Cdd:pfam04997 297 KS K RP L KSI SQ RLK G KEGR F RGNL 320
RNA_pol_Rpb1_6
pfam04992 RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
892-1076
1.51e-93
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511
Cd Length: 188
Bit Score: 300.57
E-value: 1.51e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 892 M D AVW IE S QK L D S LK MKKSE F DRTFKYEID DE NWN -- P T YL SDEHLEDLK G IR E LRDVF D A EY SK L ET DR FQ L GTE I ATN 969
Cdd:pfam04992 1 L D GAF IE K QK I D T LK LSDAA F EKRYRLDVM DE KSG fl P G YL EEGVIKEIA G DP E VQQLL D E EY EQ L LE DR EL L REI I FPT 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 970 GDS TW P - LPVNI K R H I W NAQK T F K ID L RK I SD M HP VEIVDA V DK L QE RL L VV P GDD A LS V EAQ K NATL F F N ILLRS T LAS 1048
Cdd:pfam04992 81 GDS KV P q LPVNI Q R I I Q NAQK I F H ID D RK P SD L HP IYVIEG V RE L LD RL V VV R GDD P LS K EAQ E NATL L F K ILLRS R LAS 160
170 180
....*....|....*....|....*...
gi 334187204 1049 KRVLEEY K L SR EAF E WV I GEIESRFLQ S 1076
Cdd:pfam04992 161 KRVLEEY R L NK EAF D WV L GEIESRFLQ A 188
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1052-1466
1.75e-93
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 308.31
E-value: 1.75e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1052 LEE Y KL SR E AF E WV I G E IESRF L Q SLV A PGE MI G C VAAQSIGEP A TQMT LN TFHYAGV SAK NVTLG V PRL R EI INVA K RI 1131
Cdd:PRK04309 30 LEE R KL TE E EV E EI I E E VVREY L R SLV E PGE AV G V VAAQSIGEP G TQMT MR TFHYAGV AEI NVTLG L PRL I EI VDAR K EP 109
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1132 K TP SLSV YL TP E ASKSK E G A KT V QCAL E Y TTL RSVTQATE V wy D PDP M ST IIE edfefvrsyyempdedvspdkispwll 1211
Cdd:PRK04309 110 S TP MMTI YL KD E YAYDR E K A EE V ARKI E A TTL ENLAKDIS V -- D LAN M TI IIE --------------------------- 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1212 rie L NR EM MV D KK L SMA D IA E K I NLEFDDDL tcifn DDNAQK LI LRIRI mndegpkgelqd E S AED dvf L K K IESNML t E 1291
Cdd:PRK04309 161 --- L DE EM LE D RG L TVD D VK E A I EKKKGGEV ----- EIEGNT LI ISPKE ------------ P S YRE --- L R K LAEKIR - N 216
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1292 MALR GI PD I NK V F I K qvrksrfdeeggf K TSE E WMLD TEG V NL LA V MCH E D VD PK RTT S N HLI EI I EVLGIEA V R R A LLD 1371
Cdd:PRK04309 217 IKIK GI KG I KR V I I R ------------- K EGD E YVIY TEG S NL KE V LKV E G VD AT RTT T N NIH EI E EVLGIEA A R N A IIE 283
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1372 E LRVVISFD G SY V NY RH LAILC D T MT YR G HLMA I T RHG INRNDTGP L M R CS FE E TV DI LLDAA AYA E T D C L R GVTENI ML 1451
Cdd:PRK04309 284 E IKNTLEEQ G LD V DI RH IMLVA D M MT WD G EVRQ I G RHG VSGEKASV L A R AA FE V TV KH LLDAA VRG E V D E L K GVTENI IV 363
410
....*....|....*
gi 334187204 1452 GQ LA P I GTGD C EL YL 1466
Cdd:PRK04309 364 GQ PI P L GTGD V EL TM 378
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1042-1464
2.39e-86
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 287.33
E-value: 2.39e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1042 L RS T LASKRVLEEYK L SR eafew V I GEI E SRF L Q SL VA PGE MI G C VAAQSIGEP A TQMT LN TFHYAGV SAK NVTLG V PRL 1121
Cdd:TIGR02389 10 L EE T VKKREISDKEE L DE ----- I I KRV E EEY L R SL ID PGE AV G I VAAQSIGEP G TQMT MR TFHYAGV AEL NVTLG L PRL 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1122 R EI INVA K RIK TPS LSV YL TP E AS K SK E G A KT V QCAL E Y T T L RS V T qatevwydpdpmstiieedfefvrsyyempd E D V 1201
Cdd:TIGR02389 85 I EI VDAR K TPS TPS MTI YL ED E YE K DR E K A EE V AKKI E A T K L ED V A ------------------------------- K D I 133
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1202 S P D k ISPWLLR IEL NR E MMVDKKLSMA D IAEK I NLEFDDDLTC I FN D D N aqkl ILR I RIM N DE g P K GELQ desaeddv FL 1281
Cdd:TIGR02389 134 S I D - LADMTVI IEL DE E QLKERGITVD D VEKA I KKAKLGKVIE I DM D N N ---- TIT I KPG N PS - L K ELRK -------- LK 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1282 K KI E snmlt EMALR GI PD I NK V F I K qvrksrfdeeggf K TSE E WMLD TEG V NL LA V MCH E D VD PK RTT S N HLI EI I EVLG 1361
Cdd:TIGR02389 200 E KI K ----- NLHIK GI KG I KR V V I R ------------- K EGD E YVIY TEG S NL KE V LKL E G VD KT RTT T N DIH EI A EVLG 261
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1362 IEA V R R A LLD E LRVVISFD G SY V NY RHL AILC D T MT YR G HLMA I T RHGI NRNDTGP L M R CS FE E TV DI LLDAA AYA E T D C 1441
Cdd:TIGR02389 262 IEA A R N A IIE E IKRTLEEQ G LD V DI RHL MLVA D L MT WD G EVRQ I G RHGI SGEKASV L A R AA FE V TV KH LLDAA IRG E V D E 341
410 420
....*....|....*....|...
gi 334187204 1442 L R GV T ENI ML GQ LA P I GTGD CE L 1464
Cdd:TIGR02389 342 L K GV I ENI IV GQ PI P L GTGD VD L 364
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
10-887
5.43e-62
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain]
Cd Length: 1165
Bit Score: 233.51
E-value: 5.43e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 10 A E V SKVRVVQF G IL SP DE IR QM S VIH V EHS ET T -- EKG KP KVG GL SDT R - L G TI -------------- DRK V K CE T C MAN 72
Cdd:COG0086 2 A F V EDFDAIKI G LA SP EK IR SW S YGE V KKP ET I ny RTF KP ERD GL FCE R i F G PC kdyecycgkykrmv YKG V V CE K C GVE 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 73 M ------ A E CP GH fgy L ELA K P MY H VGFM K TVL S IMR cvcfncsk I L A D eeehkfkqa M KIKN pknr L KKI L DACKNKTK 146
Cdd:COG0086 82 V tlskvr R E RM GH --- I ELA M P VF H IWGL K SLP S RIG -------- L L L D --------- M SLRD ---- L ERV L YFESYVVI 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 147 CD G GDDIDDV Q SHST DE PVK ------- KSRGGC GA QQP K LTIEGMKMIA E YKIQ R K kndepdqlpepa E R K Q T LGADRVL 219
Cdd:COG0086 138 DP G DTPLEKG Q LLTE DE YRE ileeygd EFVAKM GA EAI K DLLGRIDLEK E SEEL R E ------------ E L K E T TSEQKRK 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 220 SVL KR I sdadc QLL - G F NPKFA RP D WMIL E VLP IP PP PV RP S V MM D ---- ATS rsed DL THQLAMI I RH N EN LKR QEKNG 294
Cdd:COG0086 206 KLI KR L ----- KVV e A F RESGN RP E WMIL D VLP VI PP DL RP L V PL D ggrf ATS ---- DL NDLYRRV I NR N NR LKR LLELK 276
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 295 AP AH I ISEFTQL LQ FHIATY FDN ELP G QP r A T QKSG RP I KS ICSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD P TINIDE 374
Cdd:COG0086 277 AP DI I VRNEKRM LQ EAVDAL FDN GRR G RA - V T GANK RP L KS LSDM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG P ELKLHQ 355
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 375 L G V P WSI AL N L TY P ET vtpynier LKE L VDY G p HPPPG K TGA K YII R DDGQRL D L rylkkssdqhle L GYKVER H L qdgd 454
Cdd:COG0086 356 C G L P KKM AL E L FK P FI -------- YRK L EER G - LATTI K SAK K MVE R EEPEVW D I ------------ L EEVIKE H P ---- 410
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 455 f VL F NR Q P S LH KMS I M -------- G HR I RIM P Y stfrlnls V TSPY NADFDGD E M NM HVP Q S F E TRA E VLE LM MVPKC I V 526
Cdd:COG0086 411 - VL L NR A P T LH RLG I Q afepvlie G KA I QLH P L -------- V CTAF NADFDGD Q M AV HVP L S L E AQL E ARL LM LSTNN I L 481
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 527 SP QANR P VMGIV QD TL LG CRKI T KRDTFI -- E KDV F MNT --- L MWW E df D G K V PAP A IL K P R PLWT G K QV ---------- 591
Cdd:COG0086 482 SP ANGK P IIVPS QD MV LG LYYL T REREGA kg E GMI F ADP eev L RAY E -- N G A V DLH A RI K V R ITED G E QV gkivettvgr 559
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 592 -- F N L I I P KQI nllrysawhadtet G F I tpgd T QV riergellagt LC KK TLGT sngs LVHVIWEEV G PDAARK FL GHTQ 669
Cdd:COG0086 560 yl V N E I L P QEV -------------- P F Y ---- N QV ----------- IN KK HIEV ---- IIRQMYRRC G LKETVI FL DRLK 606
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 670 W L VNYWLLQN G FT IG IG D TIADSSTM E KIN E tisn A KTA VK DLIR Q FQ - G KELD PE pgrtmrdtfen R V N Q V L --- N KA R 745
Cdd:COG0086 607 K L GFKYATRA G IS IG LD D MVVPKEKQ E IFE E ---- A NKE VK EIEK Q YA e G LITE PE ----------- R Y N K V I dgw T KA S 671
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 746 DDAG S SAQKSLAET N NLKA M VTA G SK GS fin IS Q MTACV G QQNVEG K ripfg FD G RTLPH ftkddyg P ESRG F V E nsylr 825
Cdd:COG0086 672 LETE S FLMAAFSSQ N TTYM M ADS G AR GS --- AD Q LRQLA G MRGLMA K ----- PS G NIIET ------- P IGSN F R E ----- 731
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334187204 826 GL TPQ E F F FHAM G G R E GL I DTA V KT SET GY IQ RRLV KAME D IM V KYD -- GT V R N ------- SL G D VI QF L Y 887
Cdd:COG0086 732 GL GVL E Y F ISTH G A R K GL A DTA L KT ADS GY LT RRLV DVAQ D VI V TEE dc GT D R G itvtaik EG G E VI EP L K 802
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
760-1114
2.54e-09
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain]
Cd Length: 1227
Bit Score: 62.56
E-value: 2.54e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 760 N NLKA M VTA G SK G sfi N I SQ MTAC VG QQ ---- N VE G KR I pfgfdgr T LP hftkddygpesrgf VENSYLR GLT PQ E FFFH 835
Cdd:TIGR02388 119 N SVYM M AFS G AR G --- N M SQ VRQL VG MR glma N PQ G EI I ------- D LP -------------- IKTNFRE GLT VT E YVIS 174
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 836 AM G G R E GL I DTA VK T SET GY IQ RRLV KAME D IM V KYD -- GT V R nslgdviqflygedgmd AVWIESQKLDSL K MKKS ef D 913
Cdd:TIGR02388 175 SY G A R K GL V DTA LR T ADS GY LT RRLV DVSQ D VI V REE dc GT E R ----------------- SIVVRAMTEGDK K ISLG -- D 235
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 914 R TF kyeiddenwnptylsdehledlk G IRELR DV FDA E yskletdrfql G TE I ATNGDS twplpvnikrhiwnaqktfki 993
Cdd:TIGR02388 236 R LL ----------------------- G RLVAE DV LHP E ----------- G EV I VPKNTA --------------------- 260
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 994 dlrk I SDMHPVE I VD A - VDKLQE R llvvpgd DA L SV EA QKN atlffnillrstlaskrvleeyk LS R EAFE W VIGE iesr 1072
Cdd:TIGR02388 261 ---- I DPDLAKT I ET A g ISEVVV R ------- SP L TC EA ARS ----------------------- VC R KCYG W SLAH ---- 302
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 334187204 1073 fl QS LV AP GE MI G CV AAQSIGEP A TQ M T LN TFH YA GV SAKN V 1114
Cdd:TIGR02388 303 -- AH LV DL GE AV G II AAQSIGEP G TQ L T MR TFH TG GV FTGE V 342
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
826-1114
1.18e-08
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 60.39
E-value: 1.18e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 826 GLT PQ E FFFHAM G G R E GL I DTA VK T SET GY IQ RRLV KAME D IM V KYD -- GT V R n SL gdviq FLYGE D GM D A V W I esqkld 903
Cdd:PRK02597 166 GLT VT E YVISSY G A R K GL V DTA LR T ADS GY LT RRLV DVSQ D VI V REE dc GT T R - GI ----- VVEAM D DG D R V L I ------ 233
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 904 S L K mkksef DR tfkyeiddenwnptylsdehled L K G IRELR DV F D A E yskletdrfql G TE IA TNGDSTW P lpvnikrh 983
Cdd:PRK02597 234 P L G ------ DR ----------------------- L L G RVLAE DV V D P E ----------- G EV IA ERNTAID P -------- 265
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 984 iwnaqktfki DL R K isdmhpv E I VD A - V DKLQE R llvvpgd DA L SV EA Q knatlffnill RS tlaskrvleeyk LS R EAF 1062
Cdd:PRK02597 266 ---------- DL A K ------- K I EK A g V EEVMV R ------- SP L TC EA A ----------- RS ------------ VC R KCY 298
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|..
gi 334187204 1063 E W VIGEIE srflqs LV AP GE MI G CV AAQSIGEP A TQ M T LN TFH YA GV SAKN V 1114
Cdd:PRK02597 299 G W SLAHNH ------ LV DL GE AV G II AAQSIGEP G TQ L T MR TFH TG GV FTGE V 344
Name
Accession
Description
Interval
E-value
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
18-872
0e+00
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain]
Cd Length: 751
Bit Score: 1532.86
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 18 VQFGILSPDEIR Q MSV IHV EH S ET T E K G K - PK V GGL S D T R L GTIDR KVK C E TC MAN M A ECPGHFG YL ELAKP MY H V GF MK 96
Cdd:cd02733 3 VQFGILSPDEIR A MSV AEI EH P ET Y E N G G g PK L GGL N D P R M GTIDR NSR C Q TC GGD M K ECPGHFG HI ELAKP VF H I GF LT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 97 TV L S I M RCVC fncskiladeeehkfkqamkiknpknrlkkildacknktkcdggddiddvqshstdepvkksrggcgaqq 176
Cdd:cd02733 83 KI L K I L RCVC ---------------------------------------------------------------------- 92
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 177 pkltiegmkmiaeykiqrkkndepdqlpepaer K QT L G A D RVL SVL KRISD A DC QL LGF N PKF A RPDWMIL E VLP I PPP P 256
Cdd:cd02733 93 --------------------------------- K RE L S A E RVL EIF KRISD E DC RI LGF D PKF S RPDWMIL T VLP V PPP A 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 257 VRPSV M MD ATS RSEDDLTH Q LA M II RH N EN LKRQE K NGAPAHII S E FT QLLQFH I ATY F DNE L PG Q P R ATQKSGRP I KSI 336
Cdd:cd02733 140 VRPSV V MD GSA RSEDDLTH K LA D II KA N NQ LKRQE Q NGAPAHII E E DE QLLQFH V ATY M DNE I PG L P Q ATQKSGRP L KSI 219
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 337 CS RLK A KEGRIRGNLMGKRVDFSARTVITPDP TINI D EL GVP W SIA L NLT Y PE T VTP Y NI E RL K ELV DY GP HPP PG ktg A 416
Cdd:cd02733 220 RQ RLK G KEGRIRGNLMGKRVDFSARTVITPDP NLEL D QV GVP R SIA M NLT F PE I VTP F NI D RL Q ELV RN GP NEY PG --- A 296
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 417 KYIIRDDG Q R L DLRYLKK S SD Q HL EL GY K VERHLQDGD F VLFNRQPSLHKMS I MGHR IRIM PYSTFRLNLSVT S PYNADF 496
Cdd:cd02733 297 KYIIRDDG E R I DLRYLKK A SD L HL QY GY I VERHLQDGD V VLFNRQPSLHKMS M MGHR VKVL PYSTFRLNLSVT T PYNADF 376
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 497 DGDEMN M HVPQS F ETRAE VL ELMMVP KC IVSPQ A N R PVMGIVQDTLLG C RK I TKRDTF I EKD VF MN T LMW WE D F DGK V P A 576
Cdd:cd02733 377 DGDEMN L HVPQS L ETRAE LK ELMMVP RQ IVSPQ S N K PVMGIVQDTLLG V RK L TKRDTF L EKD QV MN L LMW LP D W DGK I P Q 456
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 577 PAILKP R PLWTGKQ V F N LIIPK QI NL L R Y S AW H a D TETGF I T PGDT Q V R IE R GELL A G T LCKKT L G T S N G S L V HVIW E E V 656
Cdd:cd02733 457 PAILKP K PLWTGKQ I F S LIIPK IN NL I R S S SH H - D GDKKW I S PGDT K V I IE N GELL S G I LCKKT V G A S S G G L I HVIW L E Y 535
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 657 GP D AAR K F L G HT Q WL VN Y WLL Q NGF T IGIGDTIAD SS TM E KI N ETI SN AK TA V KD LI RQF Q GK EL D P E PG R T M R DT FEN R 736
Cdd:cd02733 536 GP E AAR D F I G NI Q RV VN N WLL H NGF S IGIGDTIAD KE TM K KI Q ETI KK AK RD V IK LI EKA Q NG EL E P Q PG K T L R ES FEN K 615
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 737 VN QV LNKARD D AG S SAQKSL A E T NN L KAMVTAGSKGSFINISQ MT ACVGQQNVEGKRIPFGF DG RTLPHF T KDDYGPESR 816
Cdd:cd02733 616 VN RI LNKARD K AG K SAQKSL S E D NN F KAMVTAGSKGSFINISQ II ACVGQQNVEGKRIPFGF RR RTLPHF I KDDYGPESR 695
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 334187204 817 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT S ETGYIQRRLVKAMED I MVKYD 872
Cdd:cd02733 696 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT A ETGYIQRRLVKAMED V MVKYD 751
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
9-893
0e+00
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain]
Cd Length: 861
Bit Score: 1006.00
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 9 P AEVSKVR vvq FG I LSP D EIR Q MSV IHVEHSE T - T E K G K P KV GGL S D T RLG T I DRKVK C E TC MANMA ECPGHFG YL ELA K 87
Cdd:cd02582 1 P KRIKGIK --- FG L LSP E EIR K MSV VEIITPD T y D E D G Y P IE GGL M D P RLG V I EPGLR C K TC GNTAG ECPGHFG HI ELA R 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 88 P MY HVGF M K TVLSIM R CV C FN C SK IL AD EEE ---- HKFKQAM K I K N P --- K NRLK K ILDAC K NKTK C dggddiddvq S H s 160
Cdd:cd02582 78 P VI HVGF A K HIYDLL R AT C RS C GR IL LP EEE ieky LERIRRL K E K W P elv K RVIE K VKKKA K KRKV C ---------- P H - 146
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 161 tdepvkksrgg CGA Q Q P K L tiegm K MIAEYKIQRK K NDEPDQ L p E P A E rkqtlgadr VLSV L KR I S D A D CQ LLG FN PK F A 240
Cdd:cd02582 147 ----------- CGA P Q Y K I ----- K LEKPTTFYEE K EEGEVK L - T P S E --------- IRER L EK I P D E D LE LLG ID PK T A 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 241 RP D WM I L E VLP I PP PP VRPS VMMDATS RSEDDLTH Q L AM IIR H N EN LK RQEKN GAP AH II SEFTQ LLQ F H IA TYFDNE L P 320
Cdd:cd02582 201 RP E WM V L T VLP V PP VT VRPS ITLETGE RSEDDLTH K L VD IIR I N QR LK ENIEA GAP QL II EDLWD LLQ Y H VT TYFDNE I P 280
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 321 G Q P R A TQK SGRP I K SICS RLK A KEGR I RGNL M GKRV D FSARTVI T PDP TIN I D E L GVP WS IA LN LT Y PE T VT PY NIE RLK 400
Cdd:cd02582 281 G I P P A RHR SGRP L K TLAQ RLK G KEGR F RGNL S GKRV N FSARTVI S PDP NLS I N E V GVP ED IA KE LT V PE R VT EW NIE KMR 360
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 401 E LV DY GP HPP PG ktg A K Y I IR D DG Q R LD LRY L - KKSSDQH LE L G YK VERHL Q DGD F VLFNRQPSLH K MSIM G HR I R IM P Y 479
Cdd:cd02582 361 K LV LN GP DKW PG --- A N Y V IR P DG R R IR LRY V n REELAER LE P G WI VERHL I DGD I VLFNRQPSLH R MSIM A HR V R VL P G 437
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 480 S TFRLNL S V TS PYNADFDGDEMN M HVPQS F E T RAE VL ELM M V PKC I V SP QANR P VM G IV QD TLL G CRKI T KRD T FIE K DV 559
Cdd:cd02582 438 K TFRLNL A V CP PYNADFDGDEMN L HVPQS E E A RAE AR ELM L V QEH I L SP RYGG P II G GI QD YIS G AYLL T RKT T LFT K EE 517
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 560 FMNT L MW w EDF DG KV P A PAIL K P R PLWTGKQ V F N L II PK QI N LLRYSAW -- HADTETGFIT P G D TQ V R I ER G E LL A G TLC 637
Cdd:cd02582 518 ALQL L SA - AGY DG LL P E PAIL E P K PLWTGKQ L F S L FL PK DL N FEGKAKV cs GCSECKDEDC P N D GY V V I KN G K LL E G VID 596
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 638 KK TL G T - SN GSL V H V I WE E V G PDA AR K FL GHTQW L VNYWLLQN GFTIGI G D TIADSSTMEK I N E T I SN A KTA V KD LI R Q F 716
Cdd:cd02582 597 KK AI G A e QP GSL L H R I AK E Y G NEV AR R FL DSVTR L AIRFIELR GFTIGI D D EDIPEEARKE I E E I I KE A EKK V YE LI E Q Y 676
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 717 QGK EL D P E PGRT MRD T F E NRVN QVL N KARD D AG SS A Q K S L AET NN LKA M VTA G SK GS FI N IS QM T AC V GQQ N V E G K RI PF 796
Cdd:cd02582 677 KNG EL E P L PGRT LEE T L E MKIM QVL G KARD E AG KV A S K Y L DPF NN AVI M ART G AR GS ML N LT QM A AC L GQQ S V R G E RI NR 756
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 797 G FDG RTLPHF TKD D Y GPE S RGFV EN S YLR GL T P Q EFFFHAMGGREGL I DTAV K TS ET GY I QRRL VK A ME D IM V K YDGTVR 876
Cdd:cd02582 757 G YRN RTLPHF KPG D L GPE A RGFV RS S FRD GL S P T EFFFHAMGGREGL V DTAV R TS QS GY M QRRL IN A LQ D LY V E YDGTVR 836
890
....*....|....*..
gi 334187204 877 N S L G DV IQF L YGEDG M D 893
Cdd:cd02582 837 D S R G NI IQF K YGEDG V D 853
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
8-893
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 989.36
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 8 S P AEVSKVR vvq FG I LSP D EIR Q MSV IHVEHSE T - TEK G K P KV GGL S D T RLG T ID RKVK C E TC MANMA ECPGHFG YL ELA 86
Cdd:PRK08566 5 I P KRIGSIK --- FG L LSP E EIR K MSV TKIITAD T y DDD G Y P ID GGL M D P RLG V ID PGLR C K TC GGRAG ECPGHFG HI ELA 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 87 K P MY HVGF M K TVLSIM R CV C FN C SKILAD EEE hkfkqamkiknp KNRLKKI L DAC K NK tkcdg G DDI DD VQSHSTD E PV K 166
Cdd:PRK08566 82 R P VI HVGF A K LIYKLL R AT C RE C GRLKLT EEE ------------ IEEYLEK L ERL K EW ----- G SLA DD LIKEVKK E AA K 144
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 167 KSR - GG CG AQ Q P K LTI E gm K MI a EYKIQ RK KNDE pd Q L p E P AE rkqtlgadr VLSV L KR I S D A D CQ LLG F NP KF ARP D WM 245
Cdd:PRK08566 145 RMV c PH CG EK Q Y K IKF E -- K PT - TFYEE RK EGLV -- K L - T P SD --------- IRER L EK I P D E D LE LLG I NP EV ARP E WM 209
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 246 I L E VLP I PP PP VRPS VMMDATS RSEDDLTH Q L AM IIR H N EN LK RQEKN GAP AH II SEFTQ LLQ F H IA TYFDNE L PG Q P R A 325
Cdd:PRK08566 210 V L T VLP V PP VT VRPS ITLETGQ RSEDDLTH K L VD IIR I N QR LK ENIEA GAP QL II EDLWE LLQ Y H VT TYFDNE I PG I P P A 289
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 326 TQK SGRP I K SICS RLK A KEGR I RGNL M GKRV D FSARTVI T PDP TIN I D E L GVP WS IA LN LT Y PE T VT PY NIE R L K E L V DY 405
Cdd:PRK08566 290 RHR SGRP L K TLAQ RLK G KEGR F RGNL S GKRV N FSARTVI S PDP NLS I N E V GVP EA IA KE LT V PE R VT EW NIE E L R E Y V LN 369
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 406 GP HPP PG ktg A K Y I IR D DG Q R LD L RYL - K KSSDQH LE L G YK VERHL Q DGD F VLFNRQPSLH K MSIM G HR I R IM P YS TFRL 484
Cdd:PRK08566 370 GP EKH PG --- A N Y V IR P DG R R IK L TDK n K EELAEK LE P G WI VERHL I DGD I VLFNRQPSLH R MSIM A HR V R VL P GK TFRL 446
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 485 NL S V TS PYNADFDGDEMN M HVPQ SF E T RAE VLE LM M V PKC I V SP QANR P VM G IV QD TLL G CRKI T KRD T FIE K DVFMNT L 564
Cdd:PRK08566 447 NL A V CP PYNADFDGDEMN L HVPQ TE E A RAE ARI LM L V QEH I L SP RYGG P II G GI QD HIS G AYLL T RKS T LFT K EEALDL L 526
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 565 MWWEDFDGKV P A PAI LKPR P L WTGKQ V F N L II PK QI NL l RYS A --- WHA D TETGFITPG D TQ V R I ER G E LL A G TLC KK TL 641
Cdd:PRK08566 527 RAAGIDELPE P E PAI ENGK P Y WTGKQ I F S L FL PK DL NL - EFK A kic SGC D ECKKEDCEH D AY V V I KN G K LL E G VID KK AI 605
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 642 G TSN GS LVHV I WE E V GP DA AR K FL GHTQW L VNYWLLQN GFT I GI G D TIADSSTM E K I N E T I SN A KTA V KD LI RQFQGK EL 721
Cdd:PRK08566 606 G AEQ GS ILDR I VK E Y GP ER AR R FL DSVTR L AIRFIMLR GFT T GI D D EDIPEEAK E E I D E I I EE A EKR V EE LI EAYENG EL 685
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 722 D P E PGRT MRD T F E NRVN QVL N KARD D AG SS A Q K S L AET N NLKA M VTA G SK GS FI N IS QM T ACVGQQ N V E G K RI PF G FDG R 801
Cdd:PRK08566 686 E P L PGRT LEE T L E MKIM QVL G KARD E AG EI A E K Y L GLD N PAVI M ART G AR GS ML N LT QM A ACVGQQ S V R G E RI RR G YRD R 765
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 802 TLPHF TKD D Y G P E S RGFV EN SY LR GLTP Q EFFFHAMGGREGL I DTAV K TS ET GY I QRRL VK A ME D IM V K YDGTVR NSL G D 881
Cdd:PRK08566 766 TLPHF KPG D L G A E A RGFV RS SY KS GLTP T EFFFHAMGGREGL V DTAV R TS QS GY M QRRL IN A LQ D LK V E YDGTVR DTR G N 845
890
....*....|..
gi 334187204 882 VI QF L YGEDG M D 893
Cdd:PRK08566 846 IV QF K YGEDG V D 857
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
14-893
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 937.99
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 14 K VRVVQ FG I LSP D EIR Q MSV IH V EHSE T - TEK G K P KV GGL S D T RLG T I DRKVK C E TC MANMA ECPGHFG YL ELA K P MY HV 92
Cdd:TIGR02390 3 K IGSIK FG L LSP E EIR K MSV VE V VTAD T y DDD G Y P IE GGL M D P RLG V I EPGLR C K TC GGKVG ECPGHFG HI ELA R P VV HV 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 93 GF M K TVLS I M R CV C FN C SK I LAD EEE hkfkqamkiknp KNRLKKILDAC K NKTKCDGGDD I DDVQSHSTDEPVKKS rgg C 172
Cdd:TIGR02390 83 GF A K EIYK I L R AT C RK C GR I TLT EEE ------------ IEQYLEKINKL K EEGGDLASTL I EKIVKEAAKRMKCPH --- C 147
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 173 G AQ Q P K LTI E gmk MIAEYKIQR K KN D EPDQLP E PA ER kqtlgadrvlsv L KR I S D A D CQ LLG F NPK F ARP D WM I L E VLP I 252
Cdd:TIGR02390 148 G EE Q K K IKF E --- KPTYFYEEG K EG D VKLTPS E IR ER ------------ L EK I P D E D AE LLG I NPK V ARP E WM V L T VLP V 212
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 253 PP PP VRPS VMMDATS RSEDDLTH Q L AM IIR H N EN LK RQEKN GAP AH II SEFTQ LLQ F H I ATYFDNELPG Q P R A TQK SGRP 332
Cdd:TIGR02390 213 PP VT VRPS ITLETGE RSEDDLTH K L VD IIR I N QR LK ENIEA GAP QL II EDLWE LLQ Y H V ATYFDNELPG I P P A RHR SGRP 292
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 333 I K SICS RLK A KEGR I RGNL M GKRV D FSARTVI T PDP T I N I D E L GVP WS IA LN LT Y PE T VTP Y NI ER L K E L V DY GP HPP PG 412
Cdd:TIGR02390 293 L K TLAQ RLK G KEGR F RGNL S GKRV N FSARTVI S PDP N I S I N E V GVP EQ IA KE LT V PE R VTP W NI DE L R E Y V LN GP DSW PG 372
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 413 ktg A K Y I IR D DG Q R LDL R YLK K SS - DQH LE L G YK VERHL Q DGD F VLFNRQPSLH K MS I MGH RIRIM P YS TFRLNL S V TS P 491
Cdd:TIGR02390 373 --- A N Y V IR P DG R R IKI R DEN K EE l AER LE P G WV VERHL I DGD I VLFNRQPSLH R MS M MGH KVKVL P GK TFRLNL A V CP P 449
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 492 YNADFDGDEMN M HVPQ SF E T RAE VL ELM M V PKC I VS P QANR P VM G IVQ D TLL G CRKI T KRD T FIE K DV f MN T LMWWEDFD 571
Cdd:TIGR02390 450 YNADFDGDEMN L HVPQ TE E A RAE AR ELM L V EEH I LT P RYGG P II G GIH D YIS G AYLL T HKS T LFT K EE - VQ T ILGVAGYF 528
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 572 G KV P A PAI L KP RPL WTGKQ V F NLII P KQI N LLRYSAWHADTET -- GFIT P G D TQ V R I ER G E LL A G TLC KK TL G TSN G SLV 649
Cdd:TIGR02390 529 G DP P E PAI E KP KEY WTGKQ I F SAFL P EDL N FEGRAKICSGSDA ck KEEC P H D AY V V I KN G K LL K G VID KK AI G AEK G KIL 608
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 650 H V I WE E V GP D AAR K FL GHTQW L VNYWLLQN GFT I GI G D TIADSSTM E K I N E T I SN A KTA V KD LI RQFQGK EL D P E PGRT M 729
Cdd:TIGR02390 609 H R I VR E Y GP E AAR R FL DSVTR L FIRFITLR GFT T GI D D IDIPKEAK E E I E E L I EK A EKR V DN LI ERYRNG EL E P L PGRT V 688
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 730 RD T F E NRVNQ VL N KARD D AG SS A Q K S L AET N NLKA M VTA G SK GS FI NI S QM T A C VGQQ N V E G K RI PF G FDG RTLPHF T K D 809
Cdd:TIGR02390 689 EE T L E MKIME VL G KARD E AG EV A E K Y L DPE N HAVI M ART G AR GS LL NI T QM A A M VGQQ S V R G G RI RR G YRN RTLPHF K K G 768
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 810 D Y G PES RGFV EN S YLR GL T P Q E F FFHA M GGREGL I DTAV K TS ET GY I QRRL VK A ME D IM V K YDGTVR NSL G DV IQF L YGE 889
Cdd:TIGR02390 769 D I G AKA RGFV RS S FKK GL D P T E Y FFHA A GGREGL V DTAV R TS QS GY M QRRL IN A LQ D LY V E YDGTVR DTR G NL IQF K YGE 848
....
gi 334187204 890 DG M D 893
Cdd:TIGR02390 849 DG V D 852
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
23-876
0e+00
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain]
Cd Length: 816
Bit Score: 912.32
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 23 LSP DE I RQM S VIH V EHSE -- TT E KG KP KVG G LS D T RLGT I D RKVK CETC MA N M A E C P GHFGY LE L AK P MY H V G FM K TVLS 100
Cdd:cd02583 1 LSP ED I IRL S EVE V TNRN ly DI E TR KP LPY G VL D P RLGT S D KDGI CETC GL N L A D C V GHFGY IK L EL P VF H I G YF K AIIN 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 101 I MR C V C FN CS KI L AD EEE H - KF KQAM -- KIKNPKNR --- L KKIL DA CK NKT KC dggddiddvq S H stdepvkksrgg CG A 174
Cdd:cd02583 81 I LQ C I C KT CS RV L LP EEE K r KF LKRL rr PNLDNLQK kal K KKIL EK CK KVR KC ---------- P H ------------ CG L 138
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 175 QQ pkltiegmkmiaeykiqr K KNDEPDQ L pepaerkqtlgad R VL SVL K R I SDA D CQ LL GF NP KFA RP DWM IL EVL P I PP 254
Cdd:cd02583 139 LK ------------------ K AQEDLNP L ------------- K VL NLF K N I PPE D VE LL LM NP LAG RP ENL IL TRI P V PP 187
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 255 PPV RPSV M MD AT S RS - EDDLT HQ L AM II RH N ENL K RQEKN GA PAHI I S E FTQL LQ FHI A T Y FDN ELPG Q P r ATQKSGR PI 333
Cdd:cd02583 188 LCI RPSV V MD EK S GT n EDDLT VK L SE II FL N DVI K KHLEK GA KTQK I M E DWDF LQ LQC A L Y INS ELPG L P - LSMQPKK PI 266
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 334 KSI C S RLK A K E GR I RGNL M GKRVDFS A RTVI T PDP TIN ID EL GVP WSI A LN LTYPE T VT P YNIE R L KE LV DY GP -- HP pp 411
Cdd:cd02583 267 RGF C Q RLK G K Q GR F RGNL S GKRVDFS G RTVI S PDP NLR ID QV GVP EHV A KI LTYPE R VT R YNIE K L RK LV LN GP dv HP -- 344
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 412 gkt GA KYI I RD DG QRL dl RY LK KSSDQH ---- L EL G YK VERHL Q DGD F VLFNRQPSLH KM SIM G HR IRI MP YS TFR L N LS 487
Cdd:cd02583 345 --- GA NFV I KR DG GKK -- KF LK YGNRRK iare L KI G DI VERHL E DGD I VLFNRQPSLH RL SIM A HR AKV MP WR TFR F N EC 419
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 488 V TS PYNADFDGDEMN M HVPQ SF E T RAE V LELM M V PKCI V S P QANR P VMGIV QD T L LGCRKI T KR D T F IEKDV F MNTLMWW 567
Cdd:cd02583 420 V CT PYNADFDGDEMN L HVPQ TE E A RAE A LELM G V KNNL V T P RNGE P LIAAT QD F L TASYLL T SK D V F FDRAQ F CQLCSYM 499
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 568 E D -- FDGKV P A PAILKP RP LWTGKQ V F N L II ------ P KQI NL - LRYSAWHADTE tg FIT P G D TQ V R I ERG ELL A G T L C K 638
Cdd:cd02583 500 L D ge IKIDL P P PAILKP VE LWTGKQ I F S L LL rpnkks P VLV NL e AKEKSYTKKSP -- DMC P N D GY V V I RNS ELL C G R L D K 577
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 639 K TLG TSN - G SL VH V IWEEV GP D AA RKFLGHTQW L VNY WL LQN GF T IGI G D TIADSSTME K IN E TIS N AKTAVKDL I R Q FQ 717
Cdd:cd02583 578 S TLG SGS k N SL FY V LLRDY GP E AA AAAMNRLAK L SSR WL SNR GF S IGI D D VTPSKELLK K KE E LVD N GYAKCDEY I K Q YK 657
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 718 GKE L DPE PG R T MRD T F E NRVNQV L N K A R D DAG SSAQ K S L AET N NLKA M VTA GSKGS F INISQM T ACVGQQ NVE GKRIP F G 797
Cdd:cd02583 658 KGK L ELQ PG C T AEQ T L E AKISGE L S K I R E DAG KACL K E L HKS N SPLI M ALC GSKGS N INISQM I ACVGQQ IIS GKRIP N G 737
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334187204 798 F DG RTLPHF TKDDYG P ESR GFV E NS YLR GLTP Q EFFFH A M G GREGL I DTAVKT S ETGY I QRRL V KA M ED IM V K YDGTVR 876
Cdd:cd02583 738 F ED RTLPHF PRNSKT P AAK GFV A NS FYS GLTP T EFFFH T M S GREGL V DTAVKT A ETGY M QRRL M KA L ED LS V Q YDGTVR 816
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
18-1467
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 902.86
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 18 VQ FG IL SP DEI R QMSVIHVEHS E T - T E K G K P KV GGL S D T RLGTI DRKV KC E TC MANM A E CPGHFG YL ELA K P MY H VG F MK 96
Cdd:PRK14977 12 II FG LI SP ADA R KIGFAEITAP E A y D E D G L P VQ GGL L D G RLGTI EPGQ KC L TC GNLA A N CPGHFG HI ELA E P VI H IA F ID 91
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 97 TVLSIMRCV C FN C S K ILADE E EHKFKQAMKIKNPKN R L -- K K IL D acknktkcdgg D D I DDVQSHSTDEPV KK SRG -- G C 172
Cdd:PRK14977 92 NIKDLLNST C HK C A K LKLPQ E DLNVFKLIEEAHAAA R D ip E K RI D ----------- D E I IEEVRDQVKVYA KK AKE cp H C 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 173 GA Q Q PK L TI E GM kmiae YKIQR K kndepdql P E PA E RK qt L GADRVLSVLKR I S D A D CQ L L GF N PK F ARP D W MI L EVLPI 252
Cdd:PRK14977 161 GA P Q HE L EF E EP ----- TIFIE K -------- T E IE E HR -- L LPIEIRDIFEK I I D D D LE L I GF D PK K ARP E W AV L QAFLV 225
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 253 PP PPV RPS VMMDATS RSEDDLTH Q L AM II RH N EN LK RQEKN GAP AH I ISEFTQL LQ F H IA T Y FDN ELP G Q P R A TQ K - SGR 331
Cdd:PRK14977 226 PP LTA RPS IILETGE RSEDDLTH I L VD II KA N QK LK ESKDA GAP PL I VEDEVDH LQ Y H TS T F FDN ATA G I P Q A HH K g SGR 305
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 332 P I KS ICS RLK A KEGR I RGNL M GKRVDFSARTVI T PDP T I N IDE L GVP WS IA LN LT Y PE T V TPY NIE RL KELV DY GP HPP P 411
Cdd:PRK14977 306 P L KS LFQ RLK G KEGR F RGNL I GKRVDFSARTVI S PDP M I D IDE V GVP EA IA MK LT I PE I V NEN NIE KM KELV IN GP DEF P 385
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 412 G ktg A KY I IRD DG QRLD L RY L KKSSD ------- QH LE L G YK VERHL Q DGD F V L FNRQPSLHK M SI MG HR IRIM P YS TFRL 484
Cdd:PRK14977 386 G --- A NA I RKG DG TKIR L DF L EDKGK dalreaa EQ LE I G DI VERHL A DGD I V I FNRQPSLHK L SI LA HR VKVL P GA TFRL 462
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 485 NLS V TS PYNADFDGDEMN M HVPQ SFET RAE VL ELM M V PKCIV SP QANR P VM G IV QD TLLGCRK ITK R D TFIE K DVFM N TL 564
Cdd:PRK14977 463 HPA V CP PYNADFDGDEMN L HVPQ IEDA RAE AI ELM G V KDNLI SP RTGG P II G AL QD FITAAYL ITK D D ALFD K NEAS N IA 542
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 565 M w WEDFDGKV P A PAI - L K PR P L WTGKQ V F N L II PK QI N LLRYSA W H A DTETGFIT P --- GD TQ V R I ER GEL LA G TLCKKT 640
Cdd:PRK14977 543 M - LAGITDPL P E PAI k T K DG P A WTGKQ L F S L FL PK DF N FEGIAK W S A GKAGEAKD P scl GD GY V L I KE GEL IS G VIDDNI 621
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 641 L G TSNG --- SL VHV I WEEV G PDA A RK FL GHTQWLVNYWL L QN GF TI G I GD T I ADSSTMEK I NET I SNA K TA V K DLI R Q -- 715
Cdd:PRK14977 622 I G ALVE epe SL IDR I AKDY G EAV A IE FL NKILIIAKKEI L HY GF SN G P GD L I IPDEAKQE I EDD I QGM K DE V S DLI D Q rk 701
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 716 ------- FQ GKE ldp E PG R T M R -- DTF E NRVNQV L N KARD D AGSSA QKSLAET N NL K A M VTA G SK GS FI N IS Q MTACV GQ 786
Cdd:PRK14977 702 itrkiti YK GKE --- E LL R G M K ee EAL E ADIVNE L D KARD K AGSSA NDCIDAD N AG K I M AKT G AR GS MA N LA Q IAGAL GQ 778
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 787 Q NVE -------- G K R IPF G FDG R T L P HF TKD D YG P ESR GFV E N S Y LR GL TPQ EFFFHAMGGREGLID T A VK T SET GY I QR 858
Cdd:PRK14977 779 Q KRK trigfvlt G G R LHE G YKD R A L S HF QEG D DN P DAH GFV K N N Y RE GL NAA EFFFHAMGGREGLID K A RR T EDS GY F QR 858
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 859 RL VK A M EDI MVK YD G TVR NSL G DV IQF LY GEDG M D A vwies QKLD slkmkksefdrtfkyeiddenwnptylsde H L E dl 938
Cdd:PRK14977 859 RL AN A L EDI RLE YD E TVR DPH G HI IQF KF GEDG I D P ----- QKLD ------------------------------ H G E -- 901
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 939 kgirelrdvfdaeyskletdrfqlgteiatngdstwpl PV N IK R H I wna Q K TFKI D L - RKI S D mhpveivdav D KLQ E RL 1017
Cdd:PRK14977 902 -------------------------------------- AF N LE R I I --- E K QKIE D R g KGA S K ---------- D EIE E LA 930
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1018 lvvpgddalsveaq K NA T LF FN IL L RST LA S kr VLEEYK L SREAF E WVIG E IESR F LQSL V A PG EM IG CVA AQSI G EP A T 1097
Cdd:PRK14977 931 -------------- K EY T KT FN AN L PKL LA D -- AIHGAE L KEDEL E AICA E GKEG F EKAK V E PG QA IG IIS AQSI A EP G T 994
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1098 QMTL N TFH Y AG VS A KN VT L G VP R LR E IINVAKRIK TP SLSV YL TP E ASKSK E G A KTVQCA L EYTTL R SVTQATEV wydpd 1177
Cdd:PRK14977 995 QMTL R TFH A AG IK A MD VT H G LE R FI E LVDARAKPS TP TMDI YL DD E CKEDI E K A IEIARN L KELKV R ALIADSAI ----- 1069
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1178 pmstiie EDFEFVRSY ye M PD EDVSPDKIS P WLLRI E LNREMMVD KK LS M adiaekinl E FD DDL TCI fnddnaq K L I lr 1257
Cdd:PRK14977 1070 ------- DNANEIKLI -- K PD KRALENGCI P MERFA E IEAALAKG KK FE M --------- E LE DDL IIL ------- D L V -- 1122
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1258 irimndegpkgelqd E S A ED D VF L KKIES -- N MLTEMALR G I PDI NKVFIKQ V R K SRF D eeggfktse EW MLD T E G V NL L 1335
Cdd:PRK14977 1123 --------------- E A A DR D KP L ATLIA ir N KILDKPVK G V PDI ERAWVEL V E K DGR D --------- EW IIQ T S G S NL A 1178
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1336 AV MCHEDV D PKR T TS N HLI EI IEV LGIEA V R R A LLD EL RVVISFD G SY V NY R HLAILC D T M TY RG HLM AI ------ T RHG 1409
Cdd:PRK14977 1179 AV LEMKCI D IAN T IT N DCF EI AGT LGIEA A R N A IFN EL ASILEDQ G LE V DN R YIMLVA D I M CS RG TIE AI glqaag V RHG 1258
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*...
gi 334187204 1410 INRNDTG PL MRCS FE E T VDILLD AA AYA E TDCLR G VTENIML GQ LA PIG T G DCE L YLN 1467
Cdd:PRK14977 1259 FAGEKDS PL AKAA FE I T THTIAH AA LGG E IEKIK G ILDALIM GQ NI PIG S G KVD L LMD 1316
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1055-1467
0e+00
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain]
Cd Length: 410
Bit Score: 798.34
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1055 Y K L SR EAF E W VI GEIE S RF LQ SLV A PGEM I G CV AAQSIGEPATQMTLNTFH Y AGVSAKNVTLGVPRL R EIINVAK R IKTP 1134
Cdd:cd02584 1 Y R L NK EAF D W IL GEIE T RF NR SLV H PGEM V G TI AAQSIGEPATQMTLNTFH F AGVSAKNVTLGVPRL K EIINVAK N IKTP 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1135 SL S VYL T P EAS K SK E G AK TV Q CA LE Y TTL RS VT Q ATE VW YDPDP MS T I IEED F EFV R SY Y E M PDEDV SP D KI SPWLLRIE 1214
Cdd:cd02584 81 SL T VYL E P GFA K DE E K AK KI Q SR LE H TTL KD VT A ATE IY YDPDP QN T V IEED K EFV E SY F E F PDEDV EQ D RL SPWLLRIE 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1215 L N R EM M V DKKLSM AD IA E KI NL EF D DDL TC IF N DDNA Q KL IL RIRI M ND EGP K G E LQ desa EDDVFLKKIESNML TE M A L 1294
Cdd:cd02584 161 L D R KK M T DKKLSM EQ IA K KI KE EF K DDL NV IF S DDNA E KL VI RIRI I ND DEE K E E DS ---- EDDVFLKKIESNML SD M T L 236
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1295 R GI PD I N KVFI KQVR K SRF D - E E G G FK TS EEW M L D T E GVNL LA V MC H ED VDP K RTTSN HLI EI I EVLGIEA V R R ALL D EL 1373
Cdd:cd02584 237 K GI EG I R KVFI REEN K KKV D i E T G E FK KR EEW V L E T D GVNL RE V LS H PG VDP T RTTSN DIV EI F EVLGIEA A R K ALL K EL 316
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1374 R V VISFDGSYVNYRHLA I LCD T MT Y RGHLMAITRHGINR N DTGPLMRCSFEETVDILL D AAA YA ETD C L R GV T ENIMLGQ 1453
Cdd:cd02584 317 R N VISFDGSYVNYRHLA L LCD V MT Q RGHLMAITRHGINR Q DTGPLMRCSFEETVDILL E AAA FG ETD D L K GV S ENIMLGQ 396
410
....*....|....
gi 334187204 1454 LAPIGTG DCE L Y L N 1467
Cdd:cd02584 397 LAPIGTG CFD L L L D 410
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
19-872
0e+00
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain]
Cd Length: 779
Bit Score: 620.74
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 19 Q F GIL S PD EIR QM SV IHVEHSE T - TEK G K P KV GGL S D TR LG TI D RKVK C E TC MA N MAE CPGHFG YL EL AK P M Y HVG F MKT 97
Cdd:cd01435 1 S F SFY S AE EIR KL SV KEITNPV T f DSL G H P VP GGL Y D PA LG PL D KDDI C S TC GL N YLN CPGHFG HI EL PL P V Y NPL F FDL 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 98 VLSIM R CV CF N C skiladeee H K F KQ amkikn P K NRL K KILDAC K nkt KC D G G DDIDDVQSHSTDE ------- P V KKS R g 170
Cdd:cd01435 81 LYKLL R GS CF Y C --------- H R F RI ------ S K WEV K LFVAKL K --- LL D K G LLVEAAELDFGYD mffldvl L V PPN R - 141
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 171 gcga QQ P KLTIEGMKM iaeykiqrkkndepdqlpepa E RK Q T lgadrvl SV L KR I sdadcql L GF N pkfarpdwmilevl 250
Cdd:cd01435 142 ---- FR P PSFLGDKVF --------------------- E NP Q N ------- VL L SK I ------- L KD N -------------- 168
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 251 pippppvrpsvmmdatsrse DDLTHQ LA MIIRHNENL K RQEKN G APAH -- I I SEFT QL l Q FHIATY FD NEL pg Q P RATQ K 328
Cdd:cd01435 169 -------------------- QQIRDL LA SMRQAESQS K LDLIS G KTNS ek L I NAWL QL - Q SAVNEL FD STK -- A P KSGK K 225
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 329 S GRP IK SI csr L KA KEG RI R G N L MGKRV DFS AR T VI T PDP T I NID E L G V P WSI A LN LT Y PE T VTP Y N I E R L KEL V DY GP - 407
Cdd:cd01435 226 S PPG IK QL --- L EK KEG LF R M N M MGKRV NYA AR S VI S PDP F I ETN E I G I P LVF A KK LT F PE P VTP F N V E E L RQA V IN GP d 302
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 408 - H P ppgkt GA KY I IRD DG QRLD L RY L ----- K KSSDQH L E L --------- GY KV E RHL Q DGD F VL F NRQP S LHK M SIM G H 472
Cdd:cd01435 303 v Y P ----- GA NA I EDE DG RLIL L SA L seerr K ALAKLL L L L ssaklllng PK KV Y RHL L DGD V VL L NRQP T LHK P SIM A H 377
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 473 RI R IM P YS - T F RL NLSVTSP YNADFDGDEMN M H V PQS FET RAE VLELMMVPKCIVS P QANR P VM G IV QD TLLGCRKI T K R 551
Cdd:cd01435 378 KV R VL P GE k T L RL HYANCKS YNADFDGDEMN L H F PQS ELA RAE AYYIASTDNQYLV P TDGK P LR G LI QD HVVSGVLL T S R 457
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 552 DTF IEKDVFMN ------ TLMWWE D F DG KV -- PA PAILKP R PLWTGKQV F ----- NLI IPKQIN L LRYS ---- AWHADTET 614
Cdd:cd01435 458 DTF FTREEYQQ lvyaal RPLFTS D K DG RI kl LP PAILKP K PLWTGKQV I stilk NLI PGNAPL L NLSG kkkt KKKVGGGK 537
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 615 GFITPGDT QV R I ER GELL A G T L C K KTL G T S NGS LVH VIW E EV G PDA A R K F L GHTQW L VNYW L LQN GFT I GI G D TIADSST 694
Cdd:cd01435 538 WGGGSEES QV I I RN GELL T G V L D K SQF G A S AYG LVH AVY E LY G GET A G K L L SALGR L FTAY L QMR GFT C GI E D LLLTPKA 617
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 695 M EK INETISN AK TAVKDLIRQ F qgkeldpepgrtmrdt FENRV N Q V LNKARDDAGSSAQKSLAET NNL KA MV TA G S KGS F 774
Cdd:cd01435 618 D EK RRKILRK AK KLGLEAAAE F ---------------- LGLKL N K V TSSIIKACLPKGLLKPFPE NNL QL MV QS G A KGS M 681
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 775 I N I SQ MTACV GQQ NV EG K R I P FGFD G R TLP H F TKD D YG P ESR GF VENSY L R G LT PQE F FFH A M G GREGLIDTAVKTS ET G 854
Cdd:cd01435 682 V N A SQ ISCLL GQQ EL EG R R V P LMVS G K TLP S F PPY D TS P RAG GF ITDRF L T G IR PQE Y FFH C M A GREGLIDTAVKTS RS G 761
890
....*....|....*...
gi 334187204 855 Y I QR R L V K AM E DIM V K YD 872
Cdd:cd01435 762 Y L QR C L I K HL E GLK V N YD 779
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
826-1418
0e+00
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 583.93
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 826 GLTPQEFFFH A MGGREGLIDTAVKT S E T GY I QRRLVKA M ED IM V K YD G TVRNS L G DVI QFLYGEDG M D AVW IE S Q KLDSL 905
Cdd:pfam04998 1 GLTPQEFFFH T MGGREGLIDTAVKT A E S GY L QRRLVKA L ED LV V T YD D TVRNS G G EIV QFLYGEDG L D PLK IE K Q GRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 906 KMKKSEFDRT FK Y eiddenwnpt Y L S D EH L ED lkgirelrdvfd A E Y S KL etdrfqlgteiatngdstwplpvnikrhiw 985
Cdd:pfam04998 81 EFSDLKLEDK FK N ---------- D L L D DL L LL ------------ S E F S LS ------------------------------ 108
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 986 naq KTFK I DL R KI sdmhpveivdavdklqerllv VP G D D A LS V EAQ KN ATL F F NI LL R S T L A SKRV LE E YKLSRE AF EWV 1065
Cdd:pfam04998 109 --- YKKE I LV R DS --------------------- KL G R D R LS K EAQ ER ATL L F EL LL K S G L E SKRV RS E LTCNSK AF VCL 164
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1066 IGEIESRFL QSL VA PGE MI G CV AAQSIGEP A TQMTLNTFH Y AGV SA KNVTLGVPRL R EIINV A K R IK T PSL S VYL TP E AS 1145
Cdd:pfam04998 165 LCYGRLLYQ QSL IN PGE AV G II AAQSIGEP G TQMTLNTFH F AGV AS KNVTLGVPRL K EIINV S K N IK S PSL T VYL FD E VG 244
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1146 KSK E G AK T V QC A L E YT TL R SV TQAT E VW YDPDP MS T I I EE D FEF V RSYYEMP DE DV ------ SPDKISPWLL R IELNREM 1219
Cdd:pfam04998 245 REL E K AK K V YG A I E KV TL G SV VESG E IL YDPDP FN T P I IS D VKG V VKFFDII DE VT neeeid PETGLLILVI R LLKILNK 324
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1220 MVD K KLSMAD I AEK I NLEF D DDLTCIFNDDN A QKLILRIR I MN D E G PKGELQDESA E D D VF L KKIESNM L TEMA LRGIP D 1299
Cdd:pfam04998 325 SIK K VVKSEV I PRS I RNKV D EGRDIAIGEIT A FIIKISKK I RQ D T G GLRRVDELFM E E D PK L AILVASL L GNIT LRGIP G 404
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1300 I NKVFIKQVR K srfdeegg F K TSEE W M L D TEGVNLL A V MCHED - VD PK R TT SN HLI EI I E V LGIEA V R R ALL D E L R V V IS 1378
Cdd:pfam04998 405 I KRILVNEDD K -------- G K VEPD W V L E TEGVNLL R V LLVPG f VD AG R IL SN DIH EI L E I LGIEA A R N ALL N E I R N V YR 476
570 580 590 600
....*....|....*....|....*....|....*....|
gi 334187204 1379 F D G S Y V N Y RHL AILC D T MT YR G HL MAI T RHGIN RNDTGP L 1418
Cdd:pfam04998 477 F Q G I Y I N D RHL ELIA D Q MT RK G YI MAI G RHGIN KAELSA L 516
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
23-872
0e+00
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain]
Cd Length: 528
Bit Score: 574.00
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 23 L SP D EIR QM SV IH V EHS ET - TEKG - K PKV GG LS D T RLG T IDR KV KC E TC MANMAE CPGHFG YL ELAKP MY HVGF M K T V ls 100
Cdd:cd00399 1 M SP E EIR KW SV AK V IKP ET i DNRT l K AER GG KY D P RLG S IDR CE KC G TC GTGLND CPGHFG HI ELAKP VF HVGF I K K V -- 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 101 imrcvcfncskiladeeehkfkqamkiknpknrlkkildacknktkcdggddiddvqshstdepvkksrggcgaqqpklt 180
Cdd:cd00399 --------------------------------------------------------------------------------
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 181 iegmkmiaeykiqrkkndepdqlpepaerkqtlgadrvlsvlkrisdadcqllgfn P K F AR P D WMIL EV LP I ppppvrps 260
Cdd:cd00399 79 -------------------------------------------------------- P S F LG P E WMIL TC LP V -------- 94
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 261 vmmdatsrseddlthq LAMII R hnenlkrqeknga P AH II S E FTQ LLQ F H IA TY F DN ELP GQP r A TQKSGRP IK S ICS RL 340
Cdd:cd00399 95 ---------------- PPPCL R ------------- P SV II E E RWR LLQ E H VD TY L DN GIA GQP - Q TQKSGRP LR S LAQ RL 144
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 341 K A KEGR I RGNLMGKRVDFS A R T VI T PDP TINI D EL GVP W SIAL N L typetvtpynierlkelvdygphpppgktgakyii 420
Cdd:cd00399 145 K G KEGR F RGNLMGKRVDFS G R S VI S PDP NLRL D QV GVP K SIAL T L ----------------------------------- 189
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 421 rddgqrldlrylkkssdqhlelgykverhlq DGD F VLFNRQPSLHK M SIM G HR I R IM P Y STFRLN LS V T SPYNADFDGDE 500
Cdd:cd00399 190 ------------------------------- DGD P VLFNRQPSLHK L SIM A HR V R VL P G STFRLN PL V C SPYNADFDGDE 238
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 501 MN M HVPQS F E T RAE VL ELM M VP KC I V SPQ ANR P VM G IV QDTLLG CRKI T K rdtfiekdvfmntlmwwedfdgkvpapail 580
Cdd:cd00399 239 MN L HVPQS E E A RAE AR ELM L VP NN I L SPQ NGE P LI G LS QDTLLG AYLL T L ------------------------------ 288
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 581 kprplwt GKQ VFNLII P K qinllrysawhadtetgfitpgdtqvriergellagtlckktlgtsng S L V H VIWE E V GP DA 660
Cdd:cd00399 289 ------- GKQ IVSAAL P G ------------------------------------------------ G L L H TVTR E L GP EK 313
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 661 A R K F L GHT Q WLVNYW L LQN GF TI GIGD T I A D SSTM E KIN E T I SN AK TA V KDLIRQ FQ GKE L DPEP G R T MRDTF E NRVNQV 740
Cdd:cd00399 314 A A K L L SNL Q RVGFVF L TTS GF SV GIGD V I D D GVIP E EKT E L I EE AK KK V DEVEEA FQ AGL L TAQE G M T LEESL E DNILDF 393
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 741 LN K ARD D AGS S A QKS L AET --- N NLKA M VTA G S KGSFINI S QM T ACVGQQ N VEGKRIP F GF DG RTLPHF T KDDY G PE SR G 817
Cdd:cd00399 394 LN E ARD K AGS A A SVN L DLV skf N SIYV M AMS G A KGSFINI R QM S ACVGQQ S VEGKRIP R GF SD RTLPHF S KDDY S PE AK G 473
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 334187204 818 F VE NS Y L R GLTP Q E F FFHAMGGREGL I DTAVKT S E T GY I QRRLVKA M ED IM V K YD 872
Cdd:cd00399 474 F IR NS F L E GLTP L E Y FFHAMGGREGL V DTAVKT A E S GY L QRRLVKA L ED LV V H YD 528
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
243-546
1.02e-160
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 492.42
E-value: 1.02e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 243 D WMIL E VLP I PPP PV RPSV MM D ATSRS EDDLTH Q L AM II RH N EN LKR QEKN GAP AH II SEFTQ LLQ FHIA T YF DNE lp G Q 322
Cdd:smart00663 1 E WMIL T VLP V PPP CL RPSV QL D GGRFA EDDLTH L L RD II KR N NR LKR LLEL GAP SI II RNEKR LLQ EAVD T LI DNE -- G L 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 323 PRA T QKSGRP I KS ICS RLK A KEGR I R G NL M GKRVDFSAR T VITPDP TINID E L GVP WS IAL N LT Y PE T VTP Y NI ER L KE L 402
Cdd:smart00663 79 PRA N QKSGRP L KS LSQ RLK G KEGR F R Q NL L GKRVDFSAR S VITPDP NLKLN E V GVP KE IAL E LT F PE I VTP L NI DK L RK L 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 403 V DY GP hpppgk T GAKYIIR dd G QRLD L RYL KKS - SDQ HL EL G YK VERH LQ DGD F VLFNRQP S LH K MSI MG HR I R IMPYS T 481
Cdd:smart00663 159 V RN GP ------ N GAKYIIR -- G KKTN L KLA KKS k IAN HL KI G DI VERH VI DGD V VLFNRQP T LH R MSI QA HR V R VLEGK T 230
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334187204 482 F RLN LS V T SPYNADFDGDEMN M HVPQS F E T RAE VL ELM M VP KC I V SP QANR P VM G IV QD T LLG CR 546
Cdd:smart00663 231 I RLN PL V C SPYNADFDGDEMN L HVPQS L E A RAE AR ELM L VP NN I L SP KNGK P II G PI QD M LLG LY 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
14-351
3.81e-126
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595
Cd Length: 320
Bit Score: 398.59
E-value: 3.81e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 14 K VRVV QFGI L SP D EIR QM SV IH V EHS ET TEK G -- KP KV GGL S D T R L GTID RKVK CETC MANMAE CPGHFG YL ELAKP MY H 91
Cdd:pfam04997 3 K IKEI QFGI A SP E EIR KW SV GE V TKP ET YNY G sl KP EE GGL L D E R M GTID KDYE CETC GKKKKD CPGHFG HI ELAKP VF H 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 92 V GF M K TV L S I MR CVC FN CSK I L A D EEEH ---- K F K QAMKIK N P K NRL K K IL DA CK N K TK C DGGDDID dvqshstdepvkk 167
Cdd:pfam04997 83 I GF F K KT L K I LE CVC KY CSK L L L D PGKP klfn K D K KRLGLE N L K MGA K A IL EL CK K K DL C EHCGGKN ------------- 149
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 168 sr G G CG A QQP KLTI EG M K MI A ey K I QRK K ND E P dqlpepaer K QT L GADR VL SVL KRISD A D CQL LGFNP KFA RP D WMIL 247
Cdd:pfam04997 150 -- G V CG S QQP VSRK EG L K LK A -- A I KKS K EE E E --------- K EI L NPEK VL KIF KRISD E D VEI LGFNP SGS RP E WMIL 216
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 248 E VLP I PPP PV RPSV MM D ATS R S EDDLTH Q L AM II RH N EN LK RQEKN GAP A HII S E FTQ LLQ F H I AT Y FDNE L PG Q P R A T Q 327
Cdd:pfam04997 217 T VLP V PPP CI RPSV QL D GGR R A EDDLTH K L RD II KR N NR LK KLLEL GAP S HII R E EWR LLQ E H V AT L FDNE I PG L P P A L Q 296
330 340
....*....|....*....|....
gi 334187204 328 KS G RP I KSI CS RLK A KEGR I RGNL 351
Cdd:pfam04997 297 KS K RP L KSI SQ RLK G KEGR F RGNL 320
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
353-521
1.43e-95
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498
Cd Length: 166
Bit Score: 305.38
E-value: 1.43e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 353 GKRVDFSARTVI T PDP TINI DE L GVP W S I A LN LT Y PE T VTPYNI E RL KE LV DY GP -- H P ppgkt GA K YIIR DD G Q R L DLR 430
Cdd:pfam00623 1 GKRVDFSARTVI S PDP NLKL DE V GVP I S F A KT LT F PE I VTPYNI K RL RQ LV EN GP nv Y P ----- GA N YIIR IN G A R R DLR 75
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 431 Y L K KSS D QH LE L G YK VERH LQ DGD F VLFNRQPSLH KM SIMGHR I R IM P YS TFRLNLSVT S PYNADFDGDEMN M HVPQS F E 510
Cdd:pfam00623 76 Y Q K RRL D KE LE I G DI VERH VI DGD V VLFNRQPSLH RL SIMGHR V R VL P GK TFRLNLSVT T PYNADFDGDEMN L HVPQS E E 155
170
....*....|.
gi 334187204 511 T RAE VL ELM M V 521
Cdd:pfam00623 156 A RAE AE ELM L V 166
RNA_pol_Rpb1_6
pfam04992 RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
892-1076
1.51e-93
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511
Cd Length: 188
Bit Score: 300.57
E-value: 1.51e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 892 M D AVW IE S QK L D S LK MKKSE F DRTFKYEID DE NWN -- P T YL SDEHLEDLK G IR E LRDVF D A EY SK L ET DR FQ L GTE I ATN 969
Cdd:pfam04992 1 L D GAF IE K QK I D T LK LSDAA F EKRYRLDVM DE KSG fl P G YL EEGVIKEIA G DP E VQQLL D E EY EQ L LE DR EL L REI I FPT 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 970 GDS TW P - LPVNI K R H I W NAQK T F K ID L RK I SD M HP VEIVDA V DK L QE RL L VV P GDD A LS V EAQ K NATL F F N ILLRS T LAS 1048
Cdd:pfam04992 81 GDS KV P q LPVNI Q R I I Q NAQK I F H ID D RK P SD L HP IYVIEG V RE L LD RL V VV R GDD P LS K EAQ E NATL L F K ILLRS R LAS 160
170 180
....*....|....*....|....*...
gi 334187204 1049 KRVLEEY K L SR EAF E WV I GEIESRFLQ S 1076
Cdd:pfam04992 161 KRVLEEY R L NK EAF D WV L GEIESRFLQ A 188
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1052-1466
1.75e-93
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 308.31
E-value: 1.75e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1052 LEE Y KL SR E AF E WV I G E IESRF L Q SLV A PGE MI G C VAAQSIGEP A TQMT LN TFHYAGV SAK NVTLG V PRL R EI INVA K RI 1131
Cdd:PRK04309 30 LEE R KL TE E EV E EI I E E VVREY L R SLV E PGE AV G V VAAQSIGEP G TQMT MR TFHYAGV AEI NVTLG L PRL I EI VDAR K EP 109
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1132 K TP SLSV YL TP E ASKSK E G A KT V QCAL E Y TTL RSVTQATE V wy D PDP M ST IIE edfefvrsyyempdedvspdkispwll 1211
Cdd:PRK04309 110 S TP MMTI YL KD E YAYDR E K A EE V ARKI E A TTL ENLAKDIS V -- D LAN M TI IIE --------------------------- 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1212 rie L NR EM MV D KK L SMA D IA E K I NLEFDDDL tcifn DDNAQK LI LRIRI mndegpkgelqd E S AED dvf L K K IESNML t E 1291
Cdd:PRK04309 161 --- L DE EM LE D RG L TVD D VK E A I EKKKGGEV ----- EIEGNT LI ISPKE ------------ P S YRE --- L R K LAEKIR - N 216
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1292 MALR GI PD I NK V F I K qvrksrfdeeggf K TSE E WMLD TEG V NL LA V MCH E D VD PK RTT S N HLI EI I EVLGIEA V R R A LLD 1371
Cdd:PRK04309 217 IKIK GI KG I KR V I I R ------------- K EGD E YVIY TEG S NL KE V LKV E G VD AT RTT T N NIH EI E EVLGIEA A R N A IIE 283
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1372 E LRVVISFD G SY V NY RH LAILC D T MT YR G HLMA I T RHG INRNDTGP L M R CS FE E TV DI LLDAA AYA E T D C L R GVTENI ML 1451
Cdd:PRK04309 284 E IKNTLEEQ G LD V DI RH IMLVA D M MT WD G EVRQ I G RHG VSGEKASV L A R AA FE V TV KH LLDAA VRG E V D E L K GVTENI IV 363
410
....*....|....*
gi 334187204 1452 GQ LA P I GTGD C EL YL 1466
Cdd:PRK04309 364 GQ PI P L GTGD V EL TM 378
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1051-1467
2.03e-93
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain]
Cd Length: 363
Bit Score: 307.64
E-value: 2.03e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1051 VL E E YK L SREAF E WV I G E IESRF L Q SL VA PGE MI G C VAAQSIGEP A TQMTL N TFHYAGV SAK NVTLG V PRL R EI INVA K R 1130
Cdd:cd06528 10 VL K E HG L TLSEA E EI I K E VLREY L R SL IE PGE AV G I VAAQSIGEP G TQMTL R TFHYAGV AEI NVTLG L PRL I EI VDAR K E 89
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1131 IK TP SLSV YL TP E ASKSK E G A KT V QCAL E Y TTL RSVTQATEV wy D PDP M S tiieedfefvrsyyempdedvspdkispwl 1210
Cdd:cd06528 90 PS TP TMTI YL EE E YKYDR E K A EE V ARKI E E TTL ENLAEDISI -- D LFN M R ------------------------------ 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1211 LR IEL NR EM MV D KKLSMA D IAEK I NLEF ddd LTCIFNDDNAQKLI L RIR imndegpkgelq DE S AED dvf L K K I e SNMLT 1290
Cdd:cd06528 138 IT IEL DE EM LE D RGITVD D VLKA I EKLK --- KGKVGEEGDVTLIV L KAE ------------ EP S IKE --- L R K L - AEKIL 198
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1291 EMALR GI PD I NK V FIKQVRK srfdeeggfktse E WMLD TEG V NL L AV MCH E D VDP K RTT S N HLI EI I EVLGIEA V R R A LL 1370
Cdd:cd06528 199 NTKIK GI KG I KR V IVRKEED ------------- E YVIY TEG S NL K AV LKV E G VDP T RTT T N NIH EI E EVLGIEA A R N A II 265
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1371 D E LRVVISFD G SY V NY RH LAILC D T MTY R G HLMA I T RHGI NRNDTGP L M R CS FE E TV DI LLDAA AYA E T D C LRGV T ENI M 1450
Cdd:cd06528 266 N E IKRTLEEQ G LD V DI RH IMLVA D I MTY D G EVRQ I G RHGI AGEKPSV L A R AA FE V TV KH LLDAA VRG E V D E LRGV I ENI I 345
410
....*....|....*..
gi 334187204 1451 L GQ LA P I GTGD C EL YLN 1467
Cdd:cd06528 346 V GQ PI P L GTGD V EL TMD 362
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
27-876
1.60e-91
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain]
Cd Length: 744
Bit Score: 315.11
E-value: 1.60e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 27 E I RQM SV IHVEH settekgkpk VGGLSDT RLG TIDRKVK C E TC M A - NMAE C P GHFG YLE L AKPM YH VG F MKT V LS I MRCV 105
Cdd:cd10506 5 D I EKI SV SEIKA ---------- PNQVTNP RLG LPNESGQ C T TC G A k DNKK C E GHFG VIK L PVTI YH PY F ISE V AQ I LNKI 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 106 C FN C SK I ladeeehkf KQ AM K i K N P KNR L KK ildacknktkc D GG D D I D - D V Q SHSTD ep V K K SR ggcgaqqpkltiegm 184
Cdd:cd10506 75 C PG C KS I --------- KQ KK K - K P P RET L PP ----------- D YW D F I P k D G Q QEESC -- V T K NL --------------- 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 185 kmiaey K I Q rkkndepdqlpepaerkqtlgadr V L SVL K R I sdadcq L LGFN PK FA ----- R PDWMI L EV LP I ppppvrp 259
Cdd:cd10506 117 ------ P I L ------------------------ S L AQV K K I ------ L KEID PK LI akglp R QEGLF L KC LP V ------- 153
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 260 svmmdatsrseddlthqlamiirhnenlkrqekng A P - A H IIS EFT Q ll Q F HIATY -- FD NEL pgqp RA TQ K SGRP I KSI 336
Cdd:cd10506 154 ----------------------------------- P P n C H RVT EFT H -- G F STGSR li FD ERT ---- RA YK K LVDF I GTA 192
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 337 ----- CSRLKA K eg RIRGN L M GKR VDF S A R T V ITP DP TINID E L G V P WS IA LN LT YP E T V TPY N I ERL K E LV D YGP hppp 411
Cdd:cd10506 193 nesaa SKKSGL K -- WMKDL L L GKR SGH S F R S V VVG DP YLELN E I G I P CE IA ER LT VS E R V SSW N R ERL Q E YC D LTL ---- 266
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 412 gkt GA K YI I rdd G Q R LDL R YLKKS S DQH L EL G YKVE R H L Q DGD F VL F NR Q PS L H KM S IMGHRIRIM P Y - S TFRL N LSVT S 490
Cdd:cd10506 267 --- LL K GV I --- G V R RNG R LVGVR S HNT L QI G DVIH R P L V DGD V VL V NR P PS I H QH S LIALSVKVL P T n S VVSI N PLCC S 340
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 491 P YNA DFDGD EMNMHV PQS FET RAE VL EL MMV PK CIV S P Q ANRPVMGIV QD T LL GCRKI T K R DT F IE K d VF M NT L MWWEDF 570
Cdd:cd10506 341 P FRG DFDGD CLHGYI PQS LQA RAE LE EL VAL PK QLI S S Q SGQNLLSLT QD S LL AAHLM T E R GV F LD K - AQ M QQ L QMLCPS 419
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 571 dg KV P A PAI L K -- P R -- PLWTGKQ V F NLII P KQIN llr YS AWHAD tetgfitpgdtq V R I ER GEL LA g TLCKKTLGTSNG 646
Cdd:cd10506 420 -- QL P P PAI I K sp P S ng PLWTGKQ L F QMLL P TDLD --- YS FPSNL ------------ V F I SD GEL IS - SSGGSSWLRDSE 481
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 647 SLVHV I WEEV GP DA A RK FL GHT Q W L VNY WL LQN GF TIGIG D -- TIA DS STME K IN E T IS ---------- N A K TAVK D LIR 714
Cdd:cd10506 482 GNLFS I LVKH GP GK A LD FL DSA Q G L LCE WL SMR GF SVSLS D ly LSS DS YSRQ K MI E E IS lglreaeiac N I K QLLV D SRK 561
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 715 Q F ------------ QGKELDP E PGRTMR d TFENR V NQVLNKA R d D AGSSAQ K SLAET N N L K AM VT AGSKGS FINIS Q MTA 782
Cdd:cd10506 562 D F lsgsgeendvss DVERVIY E RQKSAA - LSQAS V SAFKQVF R - D IQNLVY K YASKD N S L L AM IK AGSKGS LLKLV Q QSG 639
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 783 C V G Q Q NVEG K --- RIP ----- FGFDGRTL P HFTKD D Y ----- GPESR G F VE N S Y L R GL T P Q E F F F H AMGG R EGLIDTAVK 849
Cdd:cd10506 640 C L G L Q LSLV K lsy RIP rqlsc AAWNSQKS P RVIEK D G secte SYIPY G V VE S S F L D GL N P L E C F V H SITS R DSSFSSNAD 719
890 900
....*....|....*....|....*..
gi 334187204 850 TS et G YIQ R R L VKA M E DI M V K YDGTVR 876
Cdd:cd10506 720 LP -- G TLF R K L MFF M R DI Y V A YDGTVR 744
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1042-1464
2.39e-86
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 287.33
E-value: 2.39e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1042 L RS T LASKRVLEEYK L SR eafew V I GEI E SRF L Q SL VA PGE MI G C VAAQSIGEP A TQMT LN TFHYAGV SAK NVTLG V PRL 1121
Cdd:TIGR02389 10 L EE T VKKREISDKEE L DE ----- I I KRV E EEY L R SL ID PGE AV G I VAAQSIGEP G TQMT MR TFHYAGV AEL NVTLG L PRL 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1122 R EI INVA K RIK TPS LSV YL TP E AS K SK E G A KT V QCAL E Y T T L RS V T qatevwydpdpmstiieedfefvrsyyempd E D V 1201
Cdd:TIGR02389 85 I EI VDAR K TPS TPS MTI YL ED E YE K DR E K A EE V AKKI E A T K L ED V A ------------------------------- K D I 133
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1202 S P D k ISPWLLR IEL NR E MMVDKKLSMA D IAEK I NLEFDDDLTC I FN D D N aqkl ILR I RIM N DE g P K GELQ desaeddv FL 1281
Cdd:TIGR02389 134 S I D - LADMTVI IEL DE E QLKERGITVD D VEKA I KKAKLGKVIE I DM D N N ---- TIT I KPG N PS - L K ELRK -------- LK 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1282 K KI E snmlt EMALR GI PD I NK V F I K qvrksrfdeeggf K TSE E WMLD TEG V NL LA V MCH E D VD PK RTT S N HLI EI I EVLG 1361
Cdd:TIGR02389 200 E KI K ----- NLHIK GI KG I KR V V I R ------------- K EGD E YVIY TEG S NL KE V LKL E G VD KT RTT T N DIH EI A EVLG 261
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1362 IEA V R R A LLD E LRVVISFD G SY V NY RHL AILC D T MT YR G HLMA I T RHGI NRNDTGP L M R CS FE E TV DI LLDAA AYA E T D C 1441
Cdd:TIGR02389 262 IEA A R N A IIE E IKRTLEEQ G LD V DI RHL MLVA D L MT WD G EVRQ I G RHGI SGEKASV L A R AA FE V TV KH LLDAA IRG E V D E 341
410 420
....*....|....*....|...
gi 334187204 1442 L R GV T ENI ML GQ LA P I GTGD CE L 1464
Cdd:TIGR02389 342 L K GV I ENI IV GQ PI P L GTGD VD L 364
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1072-1460
4.51e-77
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain]
Cd Length: 300
Bit Score: 257.92
E-value: 4.51e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1072 RFLQSL V A PG EMI G CV AAQSIGEP A TQMTL N TFH Y AGV SAK N V TLGVPR LR EIIN VA K R I K TP SLSVY L tp E ASKSKEG A 1151
Cdd:cd02736 1 KYMRAK V E PG TAV G AI AAQSIGEP G TQMTL K TFH F AGV ASM N I TLGVPR IK EIIN AS K N I S TP IITAK L -- E NDRDEKS A 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1152 KT V QCAL E Y T T L RS V TQAT E VW Y D PD pmstiieedfefvr SY Y empdedvspdkispwl LR I E L NREMMVDKK LS madia 1231
Cdd:cd02736 79 RI V KGRI E K T Y L GE V ASYI E EV Y S PD -------------- DC Y ---------------- IL I K L DKKIIEKLQ LS ----- 123
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1232 e K I NL E F dddltcifnddnaqklilrir IMN degpkgelqdesaeddv F LK kies NM L TEMALR GIP DINKVF I KQV rks 1311
Cdd:cd02736 124 - K S NL Y F --------------------- LLQ ----------------- S LK ---- RK L PDVVVS GIP EVKRAV I NKD --- 157
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1312 rf DEE G GF K tseewm L DT EG VN L L AVM CHED V DPK RTTSNH LI E IIE VLGIEA V R RALLD E LRVVISFD G SYVNY RH LAI 1391
Cdd:cd02736 158 -- KKK G KY K ------ L LV EG YG L R AVM NTPG V IGT RTTSNH IM E VEK VLGIEA A R STIIN E IQYTMKSH G MSIDP RH IML 229
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334187204 1392 L C D T MT YR G HLMA ITR H GI NRNDTGP LM RC SFE E T V D I L LD AA AYAET D CLR GV T E N I ML G QLA PIGTG 1460
Cdd:cd02736 230 L A D L MT FK G EVLG ITR F GI AKMKESV LM LA SFE K T T D H L FN AA LHGRK D SIE GV S E C I IM G KPM PIGTG 298
RNA_pol_Rpb1_7
pfam04990 RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1161-1295
7.54e-73
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).
Pssm-ID: 461510 [Multi-domain]
Cd Length: 136
Bit Score: 238.97
E-value: 7.54e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1161 TTLRSVT Q ATE VW YDPDP MS T I IEED F EFV R SY Y E M PDEDV - SP D KI SPWLLRIEL N R EM M V DK K L S M A D I AEKI NL EF D 1239
Cdd:pfam04990 1 TTLRSVT A ATE IY YDPDP RN T V IEED R EFV E SY F E I PDEDV e DL D RQ SPWLLRIEL D R KK M L DK G L T M E D V AEKI KE EF G 80
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 334187204 1240 D DL TC IF N DDNA Q KL IL RIRI M NDE GP K G E L Q DES AEDDVFLK KI E S NML TEMA LR 1295
Cdd:pfam04990 81 N DL FV IF S DDNA E KL VI RIRI I NDE KE K D E E Q EDK AEDDVFLK RL E A NML DSLT LR 136
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1050-1464
5.56e-71
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 247.80
E-value: 5.56e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1050 RVLEEYK LS REAF E WVIGE I ESRFLQSL V A P G E MI G C VAAQSIGEP A TQMT LN TFHYAGV SAK NVTLG V PRL R EI INVA K 1129
Cdd:PRK14897 151 KAMKKKE LS DDEY E EILRR I REEYERAR V D P Y E AV G I VAAQSIGEP G TQMT MR TFHYAGV AEM NVTLG L PRL I EI VDAR K 230
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1130 RIK TP SLSV YL TPEASKSK E GAKT V QCAL E Y TTL RS V T qatevwydpdpmstiieedf EFVRSYY EM P dedvspdkispw 1209
Cdd:PRK14897 231 KPS TP TMTI YL KKDYREDE E KVRE V AKKI E N TTL ID V A -------------------- DIITDIA EM S ------------ 278
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1210 l LRI EL NR E M M VDKKLSMA DI AEK I - N L E F DDDLT cifnd D NAQKLI lririmndegpkg EL Q DE S aeddvf L KK IE sn M 1288
Cdd:PRK14897 279 - VVV EL DE E K M KERLIEYD DI LAA I s K L T F KTVEI ----- D DGIIRL ------------- KP Q QP S ------ F KK LY -- L 331
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1289 L T E ---- MALR GI PD I NKVFIKQVRKS R fdeeggfktse E W MLD T E G V NL LA V MCHED VDP K RT TS N HL IEI IE VLGIEA 1364
Cdd:PRK14897 332 L A E kvks LTIK GI KG I KRAIARKENDE R ----------- R W VIY T Q G S NL KD V LEIDE VDP T RT YT N DI IEI AT VLGIEA 400
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1365 V R R A LLD E LRVVISFD G SY V NY RH LAILC D T MT YR G HLM AI T RHGI NRNDTGP L M R CS FE E T VDI LL D A AAYA E T D C L R G 1444
Cdd:PRK14897 401 A R N A IIH E AKRTLQEQ G LN V DI RH IMLVA D M MT FD G SVK AI G RHGI SGEKSSV L A R AA FE I T GKH LL R A GILG E V D K L A G 480
410 420
....*....|....*....|
gi 334187204 1445 V T ENI ML GQ LAPI GTG DCE L 1464
Cdd:PRK14897 481 V A ENI IV GQ PITL GTG AVS L 500
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
21-1127
8.40e-70
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain]
Cd Length: 1140
Bit Score: 257.67
E-value: 8.40e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 21 G I L SPD E IR QM S VIH V EHS ET T -- EKG KP KVG GL SDTRL - G TID -------------- RK V K CE T C MANMA E CP --- GHF 80
Cdd:TIGR02386 5 S I A SPD T IR NW S YGE V KKP ET I ny RTL KP EKD GL FCEKI f G PTK dwecycgkykkiry KG V V CE R C GVEVT E SK vrr ERM 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 81 G YL ELA K P MY H VGFM K TVL S IMRCVCFNCS K I L ad E EEHK F KQAMKIKNPKNR L -- K KI LD A cknktkcdgg DDIDD V QS 158
Cdd:TIGR02386 85 G HI ELA A P VA H IWYF K GLP S RIGLLLDITA K E L -- E SVLY F ENYVVLDPGDTK L dk K EV LD E ---------- TEYRE V LK 152
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 159 HST D epvk KS R G G C GA QQP K LTI E GM --- K M I A E Y KIQ RKKNDEP dqlpep AE RK qtlgad RV L SV L KRISD adcqllg F 235
Cdd:TIGR02386 153 RYG D ---- GF R A G M GA EAI K ELL E KI dld K E I E E L KIQ LRESKSD ------ QK RK ------ KL L KR L EIVEA ------- F 209
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 236 NPKFA RP D WM I L E V L P IP PP PV RP S V MM D ATSRSED DL THQLAMI I RH N EN LKR QEKN GAP AH I ISEFTQL LQ FHIATY F 315
Cdd:TIGR02386 210 KDSGN RP E WM V L D V I P VI PP EL RP M V QL D GGRFATS DL NDLYRRV I NR N NR LKR LLEL GAP EI I VRNEKRM LQ EAVDAL F 289
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 316 DN ELP G Q P r ATQ K SG RP I KS ICSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD P TINIDEL G V P WSI AL N L typet VT P YN 395
Cdd:TIGR02386 290 DN GRR G K P - VVG K NN RP L KS LSDM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG P ELKMYQC G L P KKM AL E L ----- FK P FI 363
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 396 I E RL KEL vdyg PHPPPG K TGA K Y I IRD D GQRL D L rylkkssdqh LE LGY K v E RH lqdgdf VL F NR Q P S LH KMS I MGHRIR 475
Cdd:TIGR02386 364 I K RL IDR ---- ELAANI K SAK K M I EQE D PEVW D V ---------- LE DVI K - E HP ------ VL L NR A P T LH RLG I QAFEPV 422
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 476 IMPYSTF RL NLS V TSPY NADFDGD E M NM HVP Q S F E TR AE VLE LM MVPKC I VS P QANR P VMGIV QD TL LG CRKI T -- K RDT 553
Cdd:TIGR02386 423 LVEGKAI RL HPL V CTAF NADFDGD Q M AV HVP L S P E AQ AE ARA LM LASNN I LN P KDGK P IVTPS QD MV LG LYYL T te K PGA 502
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 554 FI E KDV F M N --- TLMWWE df D GKV PAP A ILKP R P ---- L W T -- G KQV FN L I I P KQI nllrys AWHA D T E tgfitpgdtqv 624
Cdd:TIGR02386 503 KG E GKI F S N vde AIRAYD -- N GKV HLH A LIGV R T sgei L E T tv G RVI FN E I L P EGF ------ PYIN D N E ----------- 563
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 625 riergellag T L C KK TL gtsn G SL VHVIW E EV G PDAARKF L GHTQW L VNYWLLQN G F TI GIG D TI ads STM EK INE t ISN 704
Cdd:TIGR02386 564 ---------- P L S KK EI ---- S SL IDLLY E VH G IEETAEM L DKIKA L GFKYATKS G T TI SAS D IV --- VPD EK YEI - LKE 625
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 705 A KTA V KDLIRQF qgkeldp EP G RTMRDTFENR V NQVLNKAR D DAGSSAQ K S L ---- AET N NLKA M VTA G SK G sfi NISQ M 780
Cdd:TIGR02386 626 A DKE V AKIQKFY ------- NK G LITDEERYRK V VSIWSETK D KVTDAMM K L L kkdt YKF N PIFM M ADS G AR G --- NISQ F 695
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 781 TACV G QQNVEG K ri P F G f D GRT LP hftkddygpesrgf VEN S YLR GLT PQ E F F FHAM G G R E GL I DTA V KT SET GY IQ RRL 860
Cdd:TIGR02386 696 RQLA G MRGLMA K -- P S G - D IIE LP -------------- IKS S FRE GLT VL E Y F ISTH G A R K GL A DTA L KT ADS GY LT RRL 758
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 861 V KAME D IM V KYD -- GT VRN - SLGDVIQ fly G E D gmdavwies QKLD SLK mkksef DR TF - K Y EID denwnptylsdehle 936
Cdd:TIGR02386 759 V DVAQ D VV V REE dc GT EEG i EVEAIVE --- G K D --------- EIIE SLK ------ DR IV g R Y SAE --------------- 805
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 937 dlkgirelr DV F D AEYS KL ETDRFQ L G TE iatngdstwplpvnikrhiwnaqktfkidlrkisdmhpv EI VDAV dklqer 1016
Cdd:TIGR02386 806 --------- DV Y D PDTG KL IAEANT L I TE --------------------------------------- EI AEKI ------ 831
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1017 llvvpgd DALSV E A qknatlffn ILL RS T L -- A S KRVLEEY ---- K L SR eafewvigeiesrfl QS LV AP GE MI G CV AAQ 1090
Cdd:TIGR02386 832 ------- ENSGI E K --------- VKV RS V L tc E S EHGVCQK cygr D L AT --------------- GK LV EI GE AV G VI AAQ 880
1130 1140 1150
....*....|....*....|....*....|....*....
gi 334187204 1091 SIGEP A TQ M T LN TFH YA GV SA -- KNV T L G V PR LR E IINV 1127
Cdd:TIGR02386 881 SIGEP G TQ L T MR TFH TG GV AG as GDI T Q G L PR VK E LFEA 919
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1072-1465
1.66e-62
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain]
Cd Length: 309
Bit Score: 216.29
E-value: 1.66e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1072 RFLQ SLV A PGE MI G CV AAQSIGEP A TQMTLNTFH Y AG VSAK NVTLG V PRLREI INV A - K R IKTPS LSVY L TP ea S KS K E G 1150
Cdd:cd02735 1 KYMR SLV E PGE AV G LL AAQSIGEP S TQMTLNTFH F AG RGEM NVTLG I PRLREI LMT A s K N IKTPS MTLP L KN -- G KS A E R 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1151 A K T VQCA L EYT TL RS V TQAT EV WY dpdpmsti I EEDF E -- F VRSYYE mpdedvspdkisp W L - LR I E L NREM mvd K KL SM 1227
Cdd:cd02735 79 A E T LKKR L SRV TL SD V VEKV EV TE -------- I LKTI E rv F KKLLGK ------------- W C e VT I K L PLSS --- P KL LL 134
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1228 AD I A EK I nlefdddltcifnddn A Q K LI lririmndegpkgelqdesaeddvflkkiesnmltema L R G IP D I NKV F I kq 1307
Cdd:cd02735 135 LS I V EK L ---------------- A R K AV -------------------------------------- I R E IP G I TRC F V -- 158
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1308 vrks RFDEE GG F kts EEWMLD TEGVNL L A VMCHE D - V D PK R TTS N HLIEIIEVL GIEA V RRA LLD E LRV V ISFD G SY V NY 1386
Cdd:cd02735 159 ---- VEEDK GG K --- TKYLVI TEGVNL A A LWKFS D i L D VN R IYT N DIHAMLNTY GIEA A RRA IVK E ISN V FKVY G IA V DP 231
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334187204 1387 RHL AILC D T MT YR G HLMAIT R H G INRN d T G PL MRC SFE E T VDI L LD A AAYAET D C L RGVTENIML G QLAPI GTG DCE L Y 1465
Cdd:cd02735 232 RHL SLIA D Y MT FE G GYRPFN R I G MESS - T S PL QKM SFE T T LAF L KK A TLNGDI D N L SSPSSRLVV G KPVNG GTG LFD L L 309
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
10-887
5.43e-62
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain]
Cd Length: 1165
Bit Score: 233.51
E-value: 5.43e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 10 A E V SKVRVVQF G IL SP DE IR QM S VIH V EHS ET T -- EKG KP KVG GL SDT R - L G TI -------------- DRK V K CE T C MAN 72
Cdd:COG0086 2 A F V EDFDAIKI G LA SP EK IR SW S YGE V KKP ET I ny RTF KP ERD GL FCE R i F G PC kdyecycgkykrmv YKG V V CE K C GVE 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 73 M ------ A E CP GH fgy L ELA K P MY H VGFM K TVL S IMR cvcfncsk I L A D eeehkfkqa M KIKN pknr L KKI L DACKNKTK 146
Cdd:COG0086 82 V tlskvr R E RM GH --- I ELA M P VF H IWGL K SLP S RIG -------- L L L D --------- M SLRD ---- L ERV L YFESYVVI 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 147 CD G GDDIDDV Q SHST DE PVK ------- KSRGGC GA QQP K LTIEGMKMIA E YKIQ R K kndepdqlpepa E R K Q T LGADRVL 219
Cdd:COG0086 138 DP G DTPLEKG Q LLTE DE YRE ileeygd EFVAKM GA EAI K DLLGRIDLEK E SEEL R E ------------ E L K E T TSEQKRK 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 220 SVL KR I sdadc QLL - G F NPKFA RP D WMIL E VLP IP PP PV RP S V MM D ---- ATS rsed DL THQLAMI I RH N EN LKR QEKNG 294
Cdd:COG0086 206 KLI KR L ----- KVV e A F RESGN RP E WMIL D VLP VI PP DL RP L V PL D ggrf ATS ---- DL NDLYRRV I NR N NR LKR LLELK 276
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 295 AP AH I ISEFTQL LQ FHIATY FDN ELP G QP r A T QKSG RP I KS ICSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD P TINIDE 374
Cdd:COG0086 277 AP DI I VRNEKRM LQ EAVDAL FDN GRR G RA - V T GANK RP L KS LSDM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG P ELKLHQ 355
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 375 L G V P WSI AL N L TY P ET vtpynier LKE L VDY G p HPPPG K TGA K YII R DDGQRL D L rylkkssdqhle L GYKVER H L qdgd 454
Cdd:COG0086 356 C G L P KKM AL E L FK P FI -------- YRK L EER G - LATTI K SAK K MVE R EEPEVW D I ------------ L EEVIKE H P ---- 410
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 455 f VL F NR Q P S LH KMS I M -------- G HR I RIM P Y stfrlnls V TSPY NADFDGD E M NM HVP Q S F E TRA E VLE LM MVPKC I V 526
Cdd:COG0086 411 - VL L NR A P T LH RLG I Q afepvlie G KA I QLH P L -------- V CTAF NADFDGD Q M AV HVP L S L E AQL E ARL LM LSTNN I L 481
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 527 SP QANR P VMGIV QD TL LG CRKI T KRDTFI -- E KDV F MNT --- L MWW E df D G K V PAP A IL K P R PLWT G K QV ---------- 591
Cdd:COG0086 482 SP ANGK P IIVPS QD MV LG LYYL T REREGA kg E GMI F ADP eev L RAY E -- N G A V DLH A RI K V R ITED G E QV gkivettvgr 559
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 592 -- F N L I I P KQI nllrysawhadtet G F I tpgd T QV riergellagt LC KK TLGT sngs LVHVIWEEV G PDAARK FL GHTQ 669
Cdd:COG0086 560 yl V N E I L P QEV -------------- P F Y ---- N QV ----------- IN KK HIEV ---- IIRQMYRRC G LKETVI FL DRLK 606
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 670 W L VNYWLLQN G FT IG IG D TIADSSTM E KIN E tisn A KTA VK DLIR Q FQ - G KELD PE pgrtmrdtfen R V N Q V L --- N KA R 745
Cdd:COG0086 607 K L GFKYATRA G IS IG LD D MVVPKEKQ E IFE E ---- A NKE VK EIEK Q YA e G LITE PE ----------- R Y N K V I dgw T KA S 671
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 746 DDAG S SAQKSLAET N NLKA M VTA G SK GS fin IS Q MTACV G QQNVEG K ripfg FD G RTLPH ftkddyg P ESRG F V E nsylr 825
Cdd:COG0086 672 LETE S FLMAAFSSQ N TTYM M ADS G AR GS --- AD Q LRQLA G MRGLMA K ----- PS G NIIET ------- P IGSN F R E ----- 731
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334187204 826 GL TPQ E F F FHAM G G R E GL I DTA V KT SET GY IQ RRLV KAME D IM V KYD -- GT V R N ------- SL G D VI QF L Y 887
Cdd:COG0086 732 GL GVL E Y F ISTH G A R K GL A DTA L KT ADS GY LT RRLV DVAQ D VI V TEE dc GT D R G itvtaik EG G E VI EP L K 802
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
241-870
1.41e-57
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain]
Cd Length: 659
Bit Score: 212.76
E-value: 1.41e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 241 RP D WMIL E VLP IP PP PV RP S V MM D ---- ATS rsed DL THQLAMI I RH N EN LK RQEKN GAP AH I ISEFTQL LQ FHIATYF D 316
Cdd:cd01609 138 RP E WMIL T VLP VI PP DL RP M V QL D ggrf ATS ---- DL NDLYRRV I NR N NR LK KLLEL GAP EI I VRNEKRM LQ EAVDALI D 213
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 317 N ELP G Q P r A T QKSG RP I KS ICSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD P TINIDEL G V P WSI AL N L typet VT P YN I 396
Cdd:cd01609 214 N GRR G K P - V T GANN RP L KS LSDM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG P ELKLHQC G L P KEM AL E L ----- FK P FV I 287
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 397 erl K EL VDY G p HP P PG K TGA K Y I I R D D GQRL D lrylkkssdq H LE lgykver HLQD G DF VL F NR Q P S LH KMS I M ------ 470
Cdd:cd01609 288 --- R EL IER G - LA P NI K SAK K M I E R K D PEVW D ---------- I LE ------- EVIK G HP VL L NR A P T LH RLG I Q afepvl 346
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 471 -- G HR I RIM P Y stfrlnls V TSPY NADFDGD E M NM HVP Q S F E TR AE VLE LM MVPKC I V SP QANR P VMGIV QD TL LG CRKI 548
Cdd:cd01609 347 ie G KA I QLH P L -------- V CTAF NADFDGD Q M AV HVP L S L E AQ AE ARV LM LSSNN I L SP ASGK P IVTPS QD MV LG LYYL 418
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 549 TK - R DTFIEKDVFMN T L mwwedfdgkvpapailkprplwt G KQV FN L I I P K qinllrysawhadt ETG FI TP gdtqvrie 627
Cdd:cd01609 419 TK e R KGDKGEGIIET T V ----------------------- G RVI FN E I L P E -------------- GLP FI NK -------- 453
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 628 rgellag TL C KK T L gtsn GS L VHVIWEEV G PDAARKF L GHTQW L VNYWLLQN G FT I G I G D TIADS stm EK i N E T I SN A KT 707
Cdd:cd01609 454 ------- TL K KK V L ---- KK L INECYDRY G LEETAEL L DDIKE L GFKYATRS G IS I S I D D IVVPP --- EK - K E I I KE A EE 518
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 708 A VK DLIR Q F - Q G KELDP E pgrtm R D tfe N R V NQVLNKARDDAGSSAQ K S L A -- ET N NLKA M VTA G SK GS FIN I S Q MTACV 784
Cdd:cd01609 519 K VK EIEK Q Y e K G LLTEE E ----- R Y --- N K V IEIWTEVTEKVADAMM K N L D kd PF N PIYM M ADS G AR GS KSQ I R Q LAGMR 590
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 785 G - QQNVE GK R I P fgfdgrt LP hftkddygpesrgf VENSYLR GLT PQ E F F FHAM G G R E GL I DTA V KT SET GY IQ RRLV KA 863
Cdd:cd01609 591 G l MAKPS GK I I E ------- LP -------------- IKSNFRE GLT VL E Y F ISTH G A R K GL A DTA L KT ADS GY LT RRLV DV 649
....*..
gi 334187204 864 ME D IM V K 870
Cdd:cd01609 650 AQ D VI V T 656
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
524-688
1.33e-56
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507
Cd Length: 158
Bit Score: 193.61
E-value: 1.33e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 524 C I V SPQ ANR P VM G IV QD TL LG CRKI T KR DTF IEKDVF M NT LM WWEDF dgkv P A PAILKP - R PLWTGKQ V F NLII P KQ IN L 602
Cdd:pfam04983 1 N I L SPQ NGK P II G PS QD MV LG AYLL T RE DTF FDREEV M QL LM YGIVL ---- P H PAILKP i K PLWTGKQ T F SRLL P NE IN P 76
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 603 LRYSAWHAD tetg FITPG D TQ V R I ER GEL LA G TLC KKT L G T S N GSL V H V I WE E V GP DAAR KFL GHT Q W L VNYW L LQN GF T 682
Cdd:pfam04983 77 KGKPKTNEE ---- DLCEN D SY V L I NN GEL IS G VID KKT V G K S L GSL I H I I YK E Y GP EETA KFL DRL Q K L GFRY L TKS GF S 152
....*.
gi 334187204 683 IGI G D T 688
Cdd:pfam04983 153 IGI D D I 158
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1097-1469
2.93e-55
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 209.36
E-value: 2.93e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1097 T QM T LN TFHYAGV SAK NVTLG V PR LR EI INVA K RIK TP SLS V Y L TP E ASKSK E G A KT V QCAL E YT TL RS V T qatevwydp 1176
Cdd:PRK14898 541 T HN T MR TFHYAGV AEI NVTLG L PR MI EI VDAR K EPS TP IMT V H L KG E YATDR E K A EE V AKKI E SL TL GD V A --------- 611
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1177 dpmstiieedfefvrsyyempd EDVS p DKISPWLLRI EL NR E MMV D KK L SMADIA E K I NLE fdddltcifnddnaqkli L 1256
Cdd:PRK14898 612 ---------------------- TSIA - IDLWTQSIKV EL DE E TLA D RG L TIESVE E A I EKK ------------------ L 650
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1257 RIR I m NDE G PKGE L QDESAEDDVFL K K I ES nm LTEMA L R GIP D I NK V FI K Q vrksrf D E EGG fkt S EE WM L D T E G V NL LA 1336
Cdd:PRK14898 651 GVK I - DRK G TVLY L KPKTPSYKALR K R I PK -- IKNIV L K GIP G I ER V LV K K ------ E E HEN --- D EE YV L Y T Q G S NL RE 718
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1337 V MCH E D VD PK RTT S N HL IEI I EVLGIEA V R R A LLD E LRVVISFD G SY V NY RHL AILC D T MT YR G HLMA I T RHG INRNDTG 1416
Cdd:PRK14898 719 V FKI E G VD TS RTT T N NI IEI Q EVLGIEA A R N A IIN E MMNTLEQQ G LE V DI RHL MLVA D I MT AD G EVKP I G RHG VAGEKGS 798
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 334187204 1417 P L M R CS FEETV DI L L DAA AYA E T D C L R GV T EN IML G QLAPI GTG DCE L YLND E 1469
Cdd:PRK14898 799 V L A R AA FEETV KH L Y DAA EHG E V D K L K GV I EN VIV G KPIKL GTG CVD L RIDR E 851
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
169-1129
1.64e-51
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 200.87
E-value: 1.64e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 169 R GG C GA QQPKLTIEGMKM iaeykiq R K KND E PDQLPEPAERKQTLG A drvlsv L KR ISDA D CQ L LGF N pkfa R P DW MIL E 248
Cdd:PRK14906 256 K GG M GA EAVRDLLDAIDL ------- E K EAE E LRAIIANGKGQKREK A ------ V KR LKVV D AF L KSG N ---- D P AD MIL D 318
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 249 V L P IP PP PV RP S V MM D ATSRSED DL THQLAMI I RH N EN LKR QEKN GAP AH I ISEFTQL LQ FHIATY FDN ELP G Q P r A T QK 328
Cdd:PRK14906 319 V I P VI PP DL RP M V QL D GGRFATS DL NDLYRRV I NR N NR LKR LLDL GAP EI I VNNEKRM LQ EAVDSL FDN GRR G R P - V T GP 397
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 329 SG RP I KS ICSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD P TINIDEL G V P WSI AL nltyp E TVT P YNIE RL K EL vdygph 408
Cdd:PRK14906 398 GN RP L KS LADM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG P HLKLHQC G L P SAM AL ----- E LFK P FVMK RL V EL ------ 466
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 409 pppgktgakyiirdd GQRLDLRYL K KSS D QHLELGYK V ERHLQDGDF VL F NR Q P S LH KMS I MGHRIRIMPYSTFR L NLS V 488
Cdd:PRK14906 467 --------------- EYAANIKAA K RAV D RGASYVWD V LEEVIQDHP VL L NR A P T LH RLG I QAFEPVLVEGKAIK L HPL V 531
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 489 TSPY NADFDGD E M NM HVP Q S FETR AE VLE LM MVPKC I V SP QAN RP VMGIV QD TLL G CRKI T K rdtfi E K D V F MNTLMWWE 568
Cdd:PRK14906 532 CTAF NADFDGD Q M AV HVP L S TQAQ AE ARV LM LSSNN I K SP AHG RP LTVPT QD MII G VYYL T T ----- E R D G F EGEGRTFA 606
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 569 DFD GK vpapailkprplwtgkqvfnliipkqin L LR Y S A w H AD TE ---- TGFITPG D TQ VR IER G E L --- L AG TLCKK T L 641
Cdd:PRK14906 607 DFD DA ---------------------------- L NA Y D A - R AD LD lqak IVVRLSR D MT VR GSY G D L eet K AG ERIET T V 657
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 642 G tsngslv HV I WEE V G P DAAR kflghtqw LV NY WLLQNGFTIGIG D TIADS ST -- M E K I NET I SNA ---------- KTA V 709
Cdd:PRK14906 658 G ------- RI I FNQ V L P EDYP -------- YL NY KMVKKDIGRLVN D CCNRY ST ae V E P I LDG I KKT gfhyatragl TVS V 722
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 710 K D --------- LIRQFQG K ---- EL D P E P G RTMRDTFENR V NQVLNK A RDDA G SSAQKSLA E T N NLKA M VTA G SK G SFIN 776
Cdd:PRK14906 723 Y D atipddkpe ILAEADE K vaai DE D Y E D G FLSERERHKQ V VDIWTE A TEEV G EAMLAGFD E D N PIYM M ADS G AR G NIKQ 802
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 777 I S Q MTACV G - QQNVE G KR I pfgfdgr T LP hftkddygpesrgf VENSYLR GL TPQ E F F FHAM G G R E GL I DTA VK T SET GY 855
Cdd:PRK14906 803 I R Q LAGMR G l MADMK G EI I ------- D LP -------------- IKANFRE GL SVL E Y F ISTH G A R K GL V DTA LR T ADS GY 861
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 856 IQ RRLV KAME D IM V KYD -- GT vrnslgdviqflyg ED G MDAVWIESQK ldslkmkksefdrtfky EI D denwnptylsde 933
Cdd:PRK14906 862 LT RRLV DVAQ D VI V REE dc GT -------------- DE G VTYPLVKPKG ----------------- DV D ------------ 898
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 934 hl ED L K G IRE L R DV F D AE yskletdrfql G TEIATN GD stwplpvnikrhiwnaqktfkidlrkisdmhpve IVDAV D K L 1013
Cdd:PRK14906 899 -- TN L I G RCL L E DV C D PN ----------- G EVLLSA GD ---------------------------------- YIESM D D L 931
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1014 QE rl LV VP G ddalsveaqknatl FFNILL R STLASK rvl E EY KLSREAFE W vig EIES R flq SL V AP G EMI G CV AAQSIG 1093
Cdd:PRK14906 932 KR -- LV EA G -------------- VTKVQI R TLMTCH --- A EY GVCQKCYG W --- DLAT R --- RP V NI G TAV G II AAQSIG 986
970 980 990
....*....|....*....|....*....|....*.
gi 334187204 1094 EP A TQ M T LN TFH YA GV SAKNV T L G V PR LR E IINVA K 1129
Cdd:PRK14906 987 EP G TQ L T MR TFH SG GV AGDDI T Q G L PR VA E LFEAR K 1022
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
241-1113
3.65e-48
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 190.52
E-value: 3.65e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 241 RP D WM I L E VLP IP PP PV RP S V MM D ATSRSED D LTHQLAMI I RH N EN LKR QEKN GAP AH I ISEFTQL LQ FHIATY FDN elp 320
Cdd:PRK09603 1622 RP E WM M L T VLP VL PP DL RP L V AL D GGKFAVS D VNELYRRV I NR N QR LKR LMEL GAP EI I VRNEKRM LQ EAVDVL FDN --- 1698
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 321 G QPRATQ K SG -- RP I KS ICSRL K A K E GR I R G NL M GKRVDFS A R T VI TPD P TINI DE L G V P WSI AL nltyp E TVT P YNIER 398
Cdd:PRK09603 1699 G RSTNAV K GA nk RP L KS LSEII K G K Q GR F R Q NL L GKRVDFS G R S VI VVG P NLKM DE C G L P KNM AL ----- E LFK P HLLSK 1773
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 399 L K E lvdygphpppgktgakyiird D G QRLD L RYL K KSSD Q HLELGYKVERHLQD G DF VL F NR Q P S LHK M SI MGHRIRIMP 478
Cdd:PRK09603 1774 L E E --------------------- R G YATT L KQA K RMIE Q KSNEVWECLQEITE G YP VL L NR A P T LHK Q SI QAFHPKLID 1832
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 479 YSTFR L NLS V T S PY NADFDGD E M NM HVP Q S F E TR AE VLE LM MVPKC I VS P QANRP V MGIV QD TL LG CRKIT -- K RDTFI E 556
Cdd:PRK09603 1833 GKAIQ L HPL V C S AF NADFDGD Q M AV HVP L S Q E AI AE CKV LM LSSMN I LL P ASGKA V AIPS QD MV LG LYYLS le K SGVKG E 1912
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 557 KDV F MN ----- T LMWWEDF D GKVPAPAILKPRPLW T -- G KQVFNL I I P KQ I NL lry SA W HA dtetgfitpgdtqvrierg 629
Cdd:PRK09603 1913 HKL F SS vneii T AIDTKEL D IHAKIRVLDQGNIIA T sa G RMIIKS I L P DF I PT --- DL W NR ------------------- 1970
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 630 ellag TLC KK TL G T sngs LV HVIWEEV G PDAARK FL GHTQW L vnywllqn GF ---- TI GI GDTIA D SS T MEKINETISN A 705
Cdd:PRK09603 1971 ----- PMK KK DI G V ---- LV DYVHKVG G IGITAT FL DNLKT L -------- GF ryat KA GI SISME D II T PKDKQKMVEK A 2033
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 706 K TA VK DLIR Q F - QG KEL D P E PGRTMR DT F enrv NQ V LN K ARDDAGSSAQ K SLAET N NLKA M VTA G SK GS FIN I S Q MT A CV 784
Cdd:PRK09603 2034 K VE VK KIQQ Q Y d QG LLT D Q E RYNKII DT W ---- TE V ND K MSKEMMTAIA K DKEGF N SIYM M ADS G AR GS AAQ I R Q LS A MR 2109
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 785 G Q qnvegkripfgfdgrtlph F TK D D y G PESRGFVENSYLR GL TPQ E F F FHAM G G R E GL I DTA V KT SET GY IQ R R L VKAM 864
Cdd:PRK09603 2110 G L ------------------- M TK P D - G SIIETPIISNFKE GL NVL E Y F NSTH G A R K GL A DTA L KT ANA GY LT R K L IDVS 2169
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 865 EDIM V KY D GTVRNSLGDVIQFLY G ED gmdav W IE S qkldslk MKKSE F D R TFKYEID D ENW N PTY L SDEH L E D LK G IREL 944
Cdd:PRK09603 2170 QNVK V VS D DCGTHEGIEITDIAV G SE ----- L IE P ------- LEERI F G R VLLEDVI D PIT N EIL L YADT L I D EE G AKKV 2237
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 945 RD vfdaeyskletdrfqlgteiatngdstwplp VN IK rhiwnaqktfkidlrkisdmhpveivdavdklqerllvvpgdd 1024
Cdd:PRK09603 2238 VE ------------------------------- AG IK ------------------------------------------- 2243
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1025 alsveaqknatlff N I LL R STLAS K rvl EEYKLSREAFEWVI GE iesrfl QSLVA PGE MI G C VAAQSIGEP A TQ M TL N TF 1104
Cdd:PRK09603 2244 -------------- S I TI R TPVTC K --- APKGVCAKCYGLNL GE ------ GKMSY PGE AV G V VAAQSIGEP G TQ L TL R TF 2300
....*....
gi 334187204 1105 H YA G VSAKN 1113
Cdd:PRK09603 2301 H VG G TASRS 2309
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
18-1460
6.59e-48
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 189.83
E-value: 6.59e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 18 V QFG I L SP DE I RQ MS VIHV E HSE T T ------- EKG K --- PK V - G GLS D TRLGTIDR K VK ------ CE T C MANMAECP --- 77
Cdd:PRK14844 1451 V SIS I A SP ES I KR MS YGEI E DVS T A nyrtfkv EKG G lfc PK I f G PVN D DECLCGKY K KR rhrgri CE K C GVEVTSSK vrr 1530
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 78 GHF G YL ELA K P MY H VG F M K TVL S IMRCVC fnc SKI L A D E E EHKFKQAMKIKN P K ---- NRLKK I LDACK N KT K CDG G dd I 153
Cdd:PRK14844 1531 ERM G HI ELA S P VA H IW F L K SLP S RIGALL --- DMS L R D I E NILYSDNYIVID P L vspf EKGEI I SEKAY N EA K DSY G -- I 1605
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 154 D DVQSHSTD E PVK ksrggcgaqqpklti E GMKMIAEYK I QRKKND E PDQLPEPAE RK QTLGAD R VLS vlkrisdadcqll 233
Cdd:PRK14844 1606 D SFVAMQGV E AIR --------------- E LLTRLDLHE I RKDLRL E LESVASEIR RK KIIKRL R IVE ------------- 1657
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 234 G F NPKFA RP D WMIL EVL PI P PP PV RP S V MMDATSRSED DL T H QLAM II RH N EN L KRQEKNGA P AHI I SEFTQL LQ FHIAT 313
Cdd:PRK14844 1658 N F IKSGN RP E WMIL TTI PI L PP DL RP L V SLESGRPAVS DL N H HYRT II NR N NR L RKLLSLNP P EIM I RNEKRM LQ EAVDS 1737
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 314 Y FDN EL pg QPRATQ K S G RP -- I KSI CSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD PT INIDEL G V P WSI AL nltyp E TV 391
Cdd:PRK14844 1738 L FDN SR -- RNALVN K A G AV gy K KSI SDM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG PT LKLNQC G L P KRM AL ----- E LF 1810
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 392 T P YNIER LK E lvd YG p HP P PG K TGA K Y I IRDDGQRL D L ry L KKSSDQ H L elgykverhlqdgdf VL F NR Q P S LH KMS I MG 471
Cdd:PRK14844 1811 K P FVYSK LK M --- YG - MA P TI K FAS K L I RAEKPEVW D M -- L EEVIKE H P --------------- VL L NR A P T LH RLG I QA 1869
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 472 HRIRIMPYSTFR L NLS V TSPY NADFDGD E M NM HVP Q S F E TRA E VLE LMM VPKCIV SP QAN RP VMGIVQ D TL LG CRKI T KR 551
Cdd:PRK14844 1870 FEPILIEGKAIQ L HPL V CTAF NADFDGD Q M AV HVP I S L E AQL E ARV LMM STNNVL SP SNG RP IIVPSK D IV LG IYYL T LQ 1949
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 552 DTFIEKDVFMNTLMWW E DF -- DG KVPAPAIL K P R PLWT --- G KQVFNL I IPKQIN L LRYSAWHADTET GF itpgdtqvri 626
Cdd:PRK14844 1950 EPKEDDLPSFGAFCEV E HS ls DG TLHIHSSI K Y R MEYI nss G ETHYKT I CTTPGR L ILWQIFPKHENL GF ---------- 2019
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 627 erg E L LAGT L CK K TL gtsn G S L V HVIWEEV G PD A ARK F LGHTQW L VNYWLLQN G FTIGIG D TIADSSTMEKIN etis N A K 706
Cdd:PRK14844 2020 --- D L INQV L TV K EI ---- T S I V DLVYRNC G QS A TVA F SDKLMV L GFEYATFS G VSFSRC D MVIPETKATHVD ---- H A R 2088
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 707 TAV K DLIR Q F Q G keldpep G RTM R DTFE N R V NQVLN K AR D DAGSSAQ K SL ------ AET N NLKA MV TA G SK GS fin I SQM 780
Cdd:PRK14844 2089 GEI K KFSM Q Y Q D ------- G LIT R SERY N K V IDEWS K CT D MIANDML K AI siydgn SKY N SVYM MV NS G AR GS --- T SQM 2158
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 781 TACV G QQNVEG K ri P F G FDGR T lphftkddyg P ESRG F V E nsylr GL TPQ E F F FHAM G G R E GL I DTA V KT SET GY IQ RRL 860
Cdd:PRK14844 2159 KQLA G MRGLMT K -- P S G EIIE T ---------- P IISN F R E ----- GL NVF E Y F NSTH G A R K GL A DTA L KT ANS GY LT RRL 2221
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 861 V KAMED - I MV K Y D GTVR N S L gd V IQFLY g E DGMDAVWI ES QK L dslkmkksef D RT FKYE I dden W NP T ylsdehledlk 939
Cdd:PRK14844 2222 V DVSQN c I VT K H D CKTK N G L -- V VRATV - E GSTIVASL ES VV L ---------- G RT AAND I ---- Y NP V ----------- 2273
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 940 g IR EL rdvfdaeyskletdrfqlgteiatngdstwplpvnikrhiwnaqktfkid L R K ISDM hpveivda V D KLQERLLV 1019
Cdd:PRK14844 2274 - TK EL -------------------------------------------------- L V K AGEL -------- I D EDKVKQIN 2294
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1020 VP G D D ALSVEAQKNATLFFNI llr ST L ASK R V L EEY K lsreafewvigeiesrflqs L V AP GE MI G CV AAQS I GEP A TQ M 1099
Cdd:PRK14844 2295 IA G L D VVKIRSPLTCEISPGV --- CS L CYG R D L ATG K -------------------- I V SI GE AV G VI AAQS V GEP G TQ L 2351
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1100 T LN TFH YA GV sakn V T L GV PRLRE I INVAKR IK TPSLSVYLTPEA ----- S K S K E ------- G AKTVQCALE Y TTLRS V T 1167
Cdd:PRK14844 2352 T MR TFH IG GV ---- M T R GV ESSNI I ASINAK IK LNNSNIIIDKNG nkivi S R S C E vvlidsl G SEKLKHSVP Y GAKLY V D 2427
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1168 QATE V ------- WY DP DPMST I I E ------- E D FEFVR S YY E MP DE D -- V S PDKISP W L L RIELN ---- R EMMV D KKLSM 1227
Cdd:PRK14844 2428 EGGS V kigdkva EW DP YTLPI I T E ktgtvsy Q D LKDGI S IT E VM DE S tg I S SKVVKD W K L YSGGA nlrp R IVLL D DNGKV 2507
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1228 ADI A EKINLEFDDDLTCIF N DDNA QK LILRIR I MNDEGPKGELQ D ESAEDDVFLKKI E SNMLT E M A LRGIP D INKV F IKQ 1307
Cdd:PRK14844 2508 MTL A SGVEACYFIPIGAVL N VQDG QK VHAGDV I TRTPRESVKTR D ITGGLPRVIELF E ARRPK E H A IVSEI D GYVA F SEK 2587
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1308 V R KSR ------- F DE EGG ---- FKTSEEWMLDT EG VNLLAVMCHE D V DP K rttsnh L IE I IE VLG I EA VRRALLD E LRV V 1376
Cdd:PRK14844 2588 D R RGK rsilikp V DE QIS pvey LVSRSKHVIVN EG DFVRKGDLLM D G DP D ------ L HD I LR VLG L EA LAHYMIS E IQQ V 2661
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1377 ISFD G SYVNYR HL AILCDT M ------ T YR G HL M AITRHG I NR ---------- NDT G ------- P LMR ------------- 1420
Cdd:PRK14844 2662 YRLQ G VRIDNK HL EVILKQ M lqkvei T DP G DT M YLVGES I DK levdrendam SNS G krpahyl P ILQ gitrasletssfi 2741
1530 1540 1550 1560
....*....|....*....|....*....|....*....|..
gi 334187204 1421 -- C SF E ET VDI L LD AA AYAET D C L R G VT EN IML G Q L A P I GTG 1460
Cdd:PRK14844 2742 sa A SF Q ET TKV L TE AA FCGKS D P L S G LK EN VIV G R L I P A GTG 2783
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
718-819
8.65e-48
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598
Cd Length: 108
Bit Score: 166.39
E-value: 8.65e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 718 GKE L DPEP G R T MRDT FE NRV N QV LNKARD D AG SS A Q KSL AET N NLKA M VTA G S KGS F INISQ MTA C V GQQNVEGKRIPFG 797
Cdd:pfam05000 7 YGK L EDIW G M T LEES FE ALI N NI LNKARD P AG NI A S KSL DPN N SIYM M ADS G A KGS I INISQ IAG C R GQQNVEGKRIPFG 86
90 100
....*....|....*....|..
gi 334187204 798 F D GRTLPHF T KDD Y GPESRGFV 819
Cdd:pfam05000 87 F S GRTLPHF K KDD E GPESRGFV 108
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
241-1125
7.30e-43
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 172.17
E-value: 7.30e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 241 R P D WMIL E V ---------- L pippppvrps V MM D ---- ATS rse D -- DL THQL am I I R h N EN LKR QEKN GAP AH I ISEFT 304
Cdd:PRK00566 223 K P E WMIL D V lpvippdlrp L ---------- V QL D ggrf ATS --- D ln DL YRRV -- I N R - N NR LKR LLEL GAP EI I VRNEK 286
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 305 QL LQ FHIATY FDN ELP G Q P r A T QKSG RP I KS ICSR LK A K E GR I R G NL M GKRVD F S A R T VI TPD P TINIDEL G V P WSI AL N 384
Cdd:PRK00566 287 RM LQ EAVDAL FDN GRR G R P - V T GPNN RP L KS LSDM LK G K Q GR F R Q NL L GKRVD Y S G R S VI VVG P ELKLHQC G L P KKM AL E 365
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 385 L TY P ET vtpynier L K E LV DY G p HPPPG K TGA K YII R D D GQRL D lrylkkssdq H LE lgy K V ER - H L qdgdf VL F NR Q P S 463
Cdd:PRK00566 366 L FK P FI -------- M K K LV ER G - LATTI K SAK K MVE R E D PEVW D ---------- V LE --- E V IK e H P ----- VL L NR A P T 418
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 464 LH KMS I M -------- G HR I RIM P ystfr L nls V TSPY NADFDGD E M NM HVP Q S F E TR AE VLE LM MVPKC I V SP QANR P V m 535
Cdd:PRK00566 419 LH RLG I Q afepvlie G KA I QLH P ----- L --- V CTAF NADFDGD Q M AV HVP L S L E AQ AE ARV LM LSSNN I L SP ANGK P I - 489
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 536 g IV -- QD TL LG CRKI T K rdtfi E KD ------- VF MNT --- L MWW E df D G K V P -- A PAILKPRPLWT ----- G KQV FN L I I 596
Cdd:PRK00566 490 - IV ps QD MV LG LYYL T R ----- E RE gakgegm VF SSP eea L RAY E -- N G E V D lh A RIKVRITSKKL vettv G RVI FN E I L 561
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 597 P K qinllrysawhadt ETG FI tpgdtqvrierge LLAGT L C KK TL gtsn GSLVHVIWEEV G PDAARK FL GH tqwlvnyw L 676
Cdd:PRK00566 562 P E -------------- GLP FI ------------- NVNKP L K KK EI ---- SKIINEVYRRY G LKETVI FL DK -------- I 602
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 677 LQN GF -------- T IGI G D - T I AD sstm EK i N E T I SN A KTA V KDLIR Q FQGKEL dpepgrtmrd T FEN R V N Q V L --- N KA 744
Cdd:PRK00566 603 KDL GF kyatrsgi S IGI D D i V I PP ---- EK - K E I I EE A EKE V AEIEK Q YRRGLI ---------- T DGE R Y N K V I diw S KA 667
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 745 R D DAGSSAQ K S L AET ---- N NLKA M VTA G SK GS FIN I S Q MT acvgqqnve G K R ipf G F ---- D G RT -- L P hftkddygpe 814
Cdd:PRK00566 668 T D EVAKAMM K N L SKD qesf N PIYM M ADS G AR GS ASQ I R Q LA --------- G M R --- G L makp S G EI ie T P ---------- 725
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 815 srgf VENSYLR GLT PQ E F F FHAM G G R E GL I DTA V KT SET GY IQ RRLV KAME D IM V KY D -- GT vrnslgdviqflyg ED G M 892
Cdd:PRK00566 726 ---- IKSNFRE GLT VL E Y F ISTH G A R K GL A DTA L KT ADS GY LT RRLV DVAQ D VI V RE D dc GT -------------- DR G I 787
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 893 DAVW I esqkldslkmkksefdrtfkye I DDEN wnptyl SD E H LE D - LK G i R E L - R DV F D A E Y skletdrfql G TE I ATN G 970
Cdd:PRK00566 788 EVTA I ---------------------- I EGGE ------ VI E P LE E r IL G - R V L a E DV V D P E T ---------- G EV I VPA G 828
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 971 D stwplpvnikrhiwnaqktf K ID LRKIS dmhpv E I VD A - VDKLQE R llvvpgd DA L SV E AQK --------- N atlffni 1040
Cdd:PRK00566 829 T -------------------- L ID EEIAD ----- K I EE A g IEEVKI R ------- SV L TC E TRH gvcakcygr D ------- 869
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1041 llrst LA SKR vleeyklsreafewvigeiesrflqs LV AP GE MI G CV AAQSIGEP A TQ M T LN TFH YA GV sak NV T L G V PR 1120
Cdd:PRK00566 870 ----- LA TGK -------------------------- LV NI GE AV G VI AAQSIGEP G TQ L T MR TFH TG GV --- DI T G G L PR 915
....*
gi 334187204 1121 LR E II 1125
Cdd:PRK00566 916 VA E LF 920
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1354-1460
1.08e-39
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain]
Cd Length: 158
Bit Score: 144.87
E-value: 1.08e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1354 I E II E V LGIEA V R RALLD E LRV V ISFD G SY V NY RH LAILC D T MTY R G H L MAI TR H G INRND T G PLMR C SFE E T VDI LLDA 1433
Cdd:cd00630 51 H E ML E A LGIEA A R ETIIR E IQK V LASQ G VS V DR RH IELIA D V MTY S G G L RGV TR S G FRASK T S PLMR A SFE K T TKH LLDA 130
90 100
....*....|....*....|....*..
gi 334187204 1434 AA YA E T D C L R GV T ENI M LG QL AP I GTG 1460
Cdd:cd00630 131 AA AG E K D E L E GV S ENI I LG RP AP L GTG 157
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
62-549
7.29e-36
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 146.43
E-value: 7.29e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 62 R KVK CE T C MANMA E CP --- GHF G YLE LA K P MY HV GFM K TVL S IM ------------ RC V C FNC SKI L -- ADEEEH K F KQ A 124
Cdd:PRK02625 82 R GIV CE R C GVEVT E SR vrr HRM G FIK LA A P VT HV WYL K GIP S YV ailldmplrdve QI V Y FNC YVV L dp GNHKNL K Y KQ L 161
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 125 MKI knpknrlkkildacknktkc D GGDD I D D v Q SHST D EPVKKSRG - G C GA QQP K LTI E GMKM iaeykiqrkk ND E PD QL 203
Cdd:PRK02625 162 LTE -------------------- D QWLE I E D - Q IYAE D SELEGEEV v G I GA EAL K RLL E DLNL ---------- EE E AE QL 210
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 204 P E pa E RKQTL G AD R V l SVL KR ISDA D cqll G F NPKFA RP D WM I L E V L P IP PP PV RP S V MM D ATSRSED DL THQLAMI I RH 283
Cdd:PRK02625 211 R E -- E IANSK G QK R A - KLI KR LRVI D ---- N F IATGS RP E WM V L D V I P VI PP DL RP M V QL D GGRFATS DL NDLYRRV I NR 283
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 284 N EN L K R QEKNG AP AH I ISEFTQL LQ FHIATYF DN ELP G QP r ATQKSG RP I KS ICSRLKA K E GR I R G NL M GKRVD F S A R T V 363
Cdd:PRK02625 284 N NR L A R LQEIL AP EI I VRNEKRM LQ EAVDALI DN GRR G RT - VVGANN RP L KS LSDIIEG K Q GR F R Q NL L GKRVD Y S G R S V 362
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 364 I TPD P TINIDEL G V P WSI A L nltyp E TVT P YN I E RL -- KEL V D ygphpp PG K TGA K Y I I R D D GQRLD lrylkkssdqhle 441
Cdd:PRK02625 363 I VVG P KLKMHQC G L P KEM A I ----- E LFQ P FV I H RL ir QGI V N ------ NI K AAK K L I Q R A D PEVWQ ------------- 418
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 442 lgyk V ERHLQD G DF VL F NR Q P S LH KMS I MGHRIRIMPYSTFR L NLS V TSPY NADFDGD E M NM HVP Q S F E TR AE VLE LM MV 521
Cdd:PRK02625 419 ---- V LEEVIE G HP VL L NR A P T LH RLG I QAFEPILVEGRAIQ L HPL V CPAF NADFDGD Q M AV HVP L S L E AQ AE ARL LM LA 494
490 500
....*....|....*....|....*...
gi 334187204 522 PKC I V SP QANR P VMGIV QD TL LGC RKI T 549
Cdd:PRK02625 495 SNN I L SP ATGE P IVTPS QD MV LGC YYL T 522
rpoC1
CHL00018 RNA polymerase beta' subunit
240-545
1.25e-34
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 143.12
E-value: 1.25e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 240 AR P D WM I L EV LP IP PP PV RP SVMM D ---- AT S rsed DL THQLAMI I RH N EN L KR - QEKNG - A P AHIISEFTQ LLQ FHIAT 313
Cdd:CHL00018 259 IE P E WM V L CL LP VL PP EL RP IIQL D ggkl MS S ---- DL NELYRRV I YR N NT L TD l LTTSR s T P GELVMCQKK LLQ EAVDA 334
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 314 YF DN ELP GQP r ATQKSGR P I KS ICSRLKA KEGR I R G NL M GKRVD F S A R T VI TPD P TINIDEL G V P WS IA LN L TY petvt P 393
Cdd:CHL00018 335 LL DN GIR GQP - MRDGHNK P Y KS FSDVIEG KEGR F R E NL L GKRVD Y S G R S VI VVG P SLSLHQC G L P RE IA IE L FQ ----- P 408
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 394 YN I ER L KEL vdygp H PPPGKTG AK YI IR DDGQRLD lrylkkssdqhlelgy KVERHLQD G DF VL F NR Q P S LH KMS I M --- 470
Cdd:CHL00018 409 FV I RG L IRQ ----- H LASNIRA AK SK IR EKEPIVW ---------------- EILQEVMQ G HP VL L NR A P T LH RLG I Q afq 467
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 471 ----- G HR I RIM P ystfrlnl S V TSPY NADFDGD E M NM HVP Q S F E TR AE VLE LM MVPKCIV SP QANR P VMGIV QD T LLG C 545
Cdd:CHL00018 468 pilve G RA I CLH P -------- L V CKGF NADFDGD Q M AV HVP L S L E AQ AE ARL LM FSHMNLL SP AIGD P ISVPS QD M LLG L 539
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1076-1134
1.35e-12
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain]
Cd Length: 204
Bit Score: 68.71
E-value: 1.35e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 334187204 1076 S LV AP GE MI G CV AAQSIGEP A TQ M T LN TFH YA GV s A KNV T L G V PR LR E IINV ak R IKT P 1134
Cdd:cd02655 1 K LV EL GE AV G II AAQSIGEP G TQ L T MR TFH TG GV - A TDI T Q G L PR VE E LFEA -- R KIN P 56
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
760-1114
2.54e-09
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain]
Cd Length: 1227
Bit Score: 62.56
E-value: 2.54e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 760 N NLKA M VTA G SK G sfi N I SQ MTAC VG QQ ---- N VE G KR I pfgfdgr T LP hftkddygpesrgf VENSYLR GLT PQ E FFFH 835
Cdd:TIGR02388 119 N SVYM M AFS G AR G --- N M SQ VRQL VG MR glma N PQ G EI I ------- D LP -------------- IKTNFRE GLT VT E YVIS 174
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 836 AM G G R E GL I DTA VK T SET GY IQ RRLV KAME D IM V KYD -- GT V R nslgdviqflygedgmd AVWIESQKLDSL K MKKS ef D 913
Cdd:TIGR02388 175 SY G A R K GL V DTA LR T ADS GY LT RRLV DVSQ D VI V REE dc GT E R ----------------- SIVVRAMTEGDK K ISLG -- D 235
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 914 R TF kyeiddenwnptylsdehledlk G IRELR DV FDA E yskletdrfql G TE I ATNGDS twplpvnikrhiwnaqktfki 993
Cdd:TIGR02388 236 R LL ----------------------- G RLVAE DV LHP E ----------- G EV I VPKNTA --------------------- 260
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 994 dlrk I SDMHPVE I VD A - VDKLQE R llvvpgd DA L SV EA QKN atlffnillrstlaskrvleeyk LS R EAFE W VIGE iesr 1072
Cdd:TIGR02388 261 ---- I DPDLAKT I ET A g ISEVVV R ------- SP L TC EA ARS ----------------------- VC R KCYG W SLAH ---- 302
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 334187204 1073 fl QS LV AP GE MI G CV AAQSIGEP A TQ M T LN TFH YA GV SAKN V 1114
Cdd:TIGR02388 303 -- AH LV DL GE AV G II AAQSIGEP G TQ L T MR TFH TG GV FTGE V 342
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1081-1461
4.38e-09
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain]
Cd Length: 381
Bit Score: 60.51
E-value: 4.38e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1081 GE MI G CV AA QS I G EPA TQMT L NTFHYAGV S A knvtlg VPR L R E II -- NVAKRI K TPSLS V Y L TPEAS K SK ------ EG A K 1152
Cdd:cd02737 1 GE PV G SL AA TA I S EPA YKAL L DPPQSLES S P ------ LEL L K E VL ec RSKSKS K ENDRR V I L SLHLC K CD hgfeye RA A L 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1153 T V QCA LE YT TL RSVTQATEVW Y D P DPMST I IE E DFEFVRSYY ----- EMPDEDVSPD K I SPW LLRIE L NR E MMVDKKL -- 1225
Cdd:cd02737 75 E V KNH LE RV TL EDLATTSMIK Y S P QATEA I VG E IGDQLNTKK kgkkk AIFSTSLKIT K F SPW VCHFH L DK E CQKLSDG pc 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1226 --- S MADIAE K --- IN L EFDD D LTCI F nddnaqkl I L RIR I MN DE GP K G - ELQD E SAEDDVFL K KIESNMLT E MA L rgip 1298
Cdd:cd02737 155 ltf S VSKEVS K sse EL L DVLR D RIIP F -------- L L ETV I KG DE RI K S v NILW E DSPSTSWV K SVGKSSRG E LV L ---- 222
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1299 din K V FIKQVR K S rfd EE G GF ktsee W -- ML D T egvn LLA VM ch EDV D PK R TTSNHLIE I IE VLGI E A VRRALLDE L RVV 1376
Cdd:cd02737 223 --- E V TVEESC K K --- TR G NA ----- W nv VM D A ---- CIP VM -- DLI D WE R SMPYSIQQ I KS VLGI D A AFEQFVQR L ESA 285
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 1377 I S FD G SY V NYR HL AILC D T MTY R G HLMAITRH G INR ----- NDTG P LMRCS F EETVDIL L D AA AYAET D C L R GV TENIML 1451
Cdd:cd02737 286 V S MT G KS V LRE HL LLVA D S MTY S G EFVGLNAK G YKA qrrsl KISA P FTEAC F SSPIKCF L K AA KKGAS D S L S GV LDACAW 365
410
....*....|
gi 334187204 1452 G QL AP I GTG D 1461
Cdd:cd02737 366 G KE AP V GTG S 375
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
826-1114
1.18e-08
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 60.39
E-value: 1.18e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 826 GLT PQ E FFFHAM G G R E GL I DTA VK T SET GY IQ RRLV KAME D IM V KYD -- GT V R n SL gdviq FLYGE D GM D A V W I esqkld 903
Cdd:PRK02597 166 GLT VT E YVISSY G A R K GL V DTA LR T ADS GY LT RRLV DVSQ D VI V REE dc GT T R - GI ----- VVEAM D DG D R V L I ------ 233
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 904 S L K mkksef DR tfkyeiddenwnptylsdehled L K G IRELR DV F D A E yskletdrfql G TE IA TNGDSTW P lpvnikrh 983
Cdd:PRK02597 234 P L G ------ DR ----------------------- L L G RVLAE DV V D P E ----------- G EV IA ERNTAID P -------- 265
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187204 984 iwnaqktfki DL R K isdmhpv E I VD A - V DKLQE R llvvpgd DA L SV EA Q knatlffnill RS tlaskrvleeyk LS R EAF 1062
Cdd:PRK02597 266 ---------- DL A K ------- K I EK A g V EEVMV R ------- SP L TC EA A ----------- RS ------------ VC R KCY 298
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|..
gi 334187204 1063 E W VIGEIE srflqs LV AP GE MI G CV AAQSIGEP A TQ M T LN TFH YA GV SAKN V 1114
Cdd:PRK02597 299 G W SLAHNH ------ LV DL GE AV G II AAQSIGEP G TQ L T MR TFH TG GV FTGE V 344
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1076-1109
6.78e-08
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 58.03
E-value: 6.78e-08
10 20 30
....*....|....*....|....*....|....
gi 334187204 1076 S LV AP GE MI G CV A A QSIGEP A TQ M TL N TFH YA GV 1109
Cdd:CHL00117 310 D LV EL GE AV G II A G QSIGEP G TQ L TL R TFH TG GV 343
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1057-1101
1.10e-07
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 57.21
E-value: 1.10e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 334187204 1057 LSR E AF E WV I G E IE S RF L QS LV A P G E MI G C VAAQSIGEP A TQM T L 1101
Cdd:PRK14898 33 VTE E MV E EI I D E VV S AY L NA LV E P Y E AV G I VAAQSIGEP G TQM S L 77
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
822-876
5.72e-06
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 51.48
E-value: 5.72e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 334187204 822 S YL R - GL TPQ E FFFHAM G G R E G LI DTAV K T SET GY IQ RRLV KAMED I M V - KY D - GT V R 876
Cdd:CHL00117 167 S NF R e GL SLT E YIISCY G A R K G VV DTAV R T ADA GY LT RRLV EVVQH I V V r ET D c GT T R 224
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
1422-1460
4.17e-04
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 45.37
E-value: 4.17e-04
10 20 30
....*....|....*....|....*....|....*....
gi 334187204 1422 SF E ET VDI L LD AA AYAET D C LRG VT EN IML G Q L A P I GTG 1460
Cdd:PRK02597 1184 SF Q ET TRV L TE AA IEGKS D W LRG LK EN VII G R L I P A GTG 1222
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1422-1460
4.98e-04
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 45.32
E-value: 4.98e-04
10 20 30
....*....|....*....|....*....|....*....
gi 334187204 1422 SF E ET VDI L LD AA AYAET D C L R G VT EN IM LG Q L A P I GTG 1460
Cdd:CHL00117 1278 SF Q ET TRV L AK AA LRGRI D W L K G LK EN VI LG G L I P A GTG 1316
Blast search parameters
Data Source:
Precalculated data, version = cdd.v.3.21
Preset Options: Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
